ACCase dataset

If you use eFindSite, please cite the following papers:
1 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
2 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
If you use eThread, please cite the following papers:
1 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
2 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
If you use eRankPPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
If you use eAromatic, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use CMS, please cite the following paper:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
If you use GeauxDockd, please cite the following papers:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
If you use eSynth, please cite the following paper:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
If you use eBoxSize, please cite the following paper:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
If you use the ACCase dataset, please cite the following paper:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
If you use eModel-BDB, please cite the following paper:
1 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
If you use eToxPred, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use eFindSitePPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
2 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
If you use TOUGH-D1, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use TOUGH-D1, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use TOUGH-M1, please cite the following paper:
1 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
If you use eMatchSite, please cite the following papers:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
If you use eMolFrag, please cite the following paper:
1 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
If you use eVolver, please cite the following papers:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
If you use eRepo-ORP, please cite the following papers:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
If you use eToxPred, please cite the following paper:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
 

Modeling data for the redesign of previously identified lead inhibitors of bacterial biotin carboxylase (BC) to expand the spectrum of organisms sensitive to amino-oxazole derivatives.

CMS

If you use eFindSite, please cite the following papers:
1 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
2 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
If you use eThread, please cite the following papers:
1 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
2 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
If you use eRankPPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
If you use eAromatic, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use CMS, please cite the following paper:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
If you use GeauxDockd, please cite the following papers:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
If you use eSynth, please cite the following paper:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
If you use eBoxSize, please cite the following paper:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
If you use the ACCase dataset, please cite the following paper:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
If you use eModel-BDB, please cite the following paper:
1 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
If you use eToxPred, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use eFindSitePPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
2 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
If you use TOUGH-D1, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use TOUGH-D1, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use TOUGH-M1, please cite the following paper:
1 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
If you use eMatchSite, please cite the following papers:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
If you use eMolFrag, please cite the following paper:
1 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
If you use eVolver, please cite the following papers:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
If you use eRepo-ORP, please cite the following papers:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
If you use eToxPred, please cite the following paper:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
 

A new metric to assess the conformational similarity based on intermolecular protein-ligand contacts. In contrast to RMSD, the Contact Mode Score, or CMS, is less dependent on the ligand size and has the ability to handle flexible receptors. Further, the eXtended Contact Mode Score, or XCMS, was developed to compare binding poses of non-identical ligands bound to different proteins.

GeauxDock

If you use eFindSite, please cite the following papers:
1 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
2 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
If you use eThread, please cite the following papers:
1 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
2 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
If you use eRankPPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
If you use eAromatic, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use CMS, please cite the following paper:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
If you use GeauxDockd, please cite the following papers:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
If you use eSynth, please cite the following paper:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
If you use eBoxSize, please cite the following paper:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
If you use the ACCase dataset, please cite the following paper:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
If you use eModel-BDB, please cite the following paper:
1 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
If you use eToxPred, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use eFindSitePPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
2 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
If you use TOUGH-D1, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use TOUGH-D1, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use TOUGH-M1, please cite the following paper:
1 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
If you use eMatchSite, please cite the following papers:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
If you use eMolFrag, please cite the following paper:
1 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
If you use eVolver, please cite the following papers:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
If you use eRepo-ORP, please cite the following papers:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
If you use eToxPred, please cite the following paper:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
 

An ultra-fast automated docking program, designed to predict how small ligands bind to pharmacologically relevant macromolecules. GeauxDock employs a novel hybrid force field, a mixed-resolution representation of protein-ligand complexes, and a Monte Carlo protocol for the efficient sampling of conformational space.

  

eAromatic

If you use eFindSite, please cite the following papers:
1 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
2 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
If you use eThread, please cite the following papers:
1 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
2 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
If you use eRankPPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
If you use eAromatic, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use CMS, please cite the following paper:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
If you use GeauxDockd, please cite the following papers:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
If you use eSynth, please cite the following paper:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
If you use eBoxSize, please cite the following paper:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
If you use the ACCase dataset, please cite the following paper:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
If you use eModel-BDB, please cite the following paper:
1 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
If you use eToxPred, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use eFindSitePPI, please cite the following papers:
1 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
2 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
If you use TOUGH-D1, please cite the following paper:
1 Pu L, Govindaraj RG, Wu HC, Brylinski M. (2019) DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 15 (2): e1006718.     
If you use TOUGH-D1, please cite the following paper:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
If you use TOUGH-M1, please cite the following paper:
1 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
If you use eMatchSite, please cite the following papers:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
If you use eMolFrag, please cite the following paper:
1 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
If you use eVolver, please cite the following papers:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
If you use eRepo-ORP, please cite the following papers:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
If you use eToxPred, please cite the following paper:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
 

A program to calculate two geometric parameters for aromatic contacts between ligands and proteins. The first parameter is the Cartesian distance between the geometric centers of two rings, referred to as the distance. The second parameter is an angle between normal vectors of two aromatic rings, referred to as the angle.

  

Structural Bioinformatics

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     

Network Pharmacology

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     

Network Biology

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     

Pharmacogenomics

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     

Cheminformatics

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     

Functional Genomics

For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Brylinski M, Lingam D. (2012) eThread: A highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures. PLoS ONE 7 (11): e50200.     
3 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
4 Brylinski M. (2015) Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling? Bio Algorithms Med Syst 11 (1): 1-7.    
For more information see:
1 Maheshwari S, Brylinski M. (2015) Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures. BMC Struct Biol 15 (1): 23.     
2 Maheshwari S, Brylinski M. (2015) Prediction of protein-protein interaction sites from weakly homologous template structures using meta-threading and machine learning. J Mol Recognit 28 (1): 35-48.     
3 Maheshwari S, Brylinski M. (2015) Predicting protein interface residues using easily accessible on-line resources. Brief Bioinform 16 (6): 1025-34.     
4 Maheshwari S, Brylinski M. (2016) Template-based identification of protein-protein interfaces using eFindSite(PPI). Methods 93: 64-71.     
5 Maheshwari S, Brylinski M. (2017) Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinformatics 18 (1): 257.     
For more information see:
1 Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. (2016) PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 32 (4): 579-86.     
2 Naderi M, Govindaraj RG, Brylinski M. (2018) eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database. GigaScience 7: 1-9.     
3 Wang C, Brylinski M, Kurgan L. (2019) PDID: database of experimental and putative drug targets in human proteome. In silico drug design: Repurposing techniques and methodologies 827-847.   
For more information see:
1 Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. (2016) A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 8: 14.     
2 Liu T, Naderi M, Alvin C, Mukhopadhyay S, Brylinski M. (2017) Break down in order to build up: Decomposing small molecules for fragment-based drug design with eMolFrag. J Chem Inf Model 57 (4): 627-631.     
For more information see:
1 Feinstein WP, Brylinski M. (2015) Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J Cheminform 7 (1): 18.     
For more information see:
1 Jambunathan N, Charles AS, Subramanian R, Saied AA, Naderi M, Rider P, Brylinski M, Chouljenko VN, Kousoulas KG. (2016) Deletion of a predicted β-sheet domain within the amino terminus of herpes simplex virus glycoprotein K conserved among alphaherpesviruses prevents virus entry into neuronal axons. J Virol 90 (5): 2230-9.     
2 Chouljenko DV, Jambunathan N, Chouljenko VN, Naderi M, Brylinski M, Caskey JR, Kousoulas KG. (2016) Herpes simplex virus type 1 UL37 protein tyrosine residues conserved among all alphaherpesviruses are required for interactions with glycoprotein K (gK), cytoplasmic virion envelopment, and infectious virus production. J Virol 90 (22): 10351-61.     
3 Rider P, Naderi M, Bergeron S, Chouljenko VN, Brylinski M, Kousoulas KG. (2017) Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection. J Virol 91 (21): e00873-17.     
For more information see:
1 Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. (2015) GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 36 (27): 2013-26.     
2 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
For more information see:
1 Ding Y, Fang Y, Moreno J, Ramanujam J, Jarrell M, Brylinski M. (2016) Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 64: 403-13.     
For more information see:
1 Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. (2018) Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 4: 13.     
2 Brylinski M, Naderi M, Govindaraj RG, Lemoine J. (2018) eRepo-ORP: Exploring the opportunity space to combat orphan diseases with existing drugs. J Mol Biol 430 (15): 2266-2273.     
For more information see:
1 Brylinski M. (2018) Aromatic interactions at the ligand-protein interface: Implications for the development of docking scoring functions. Chem Biol Drug Des 91 (2): 380-90.     
For more information see:
1 Pu L, Naderi M, Liu T, Wu HC, Mukhopadhyay S, Brylinski M. (2019) eToxPred: A machine learning-based approach to estimate the toxicity of drug candidates. BMC Pharmacol Toxicol 20 (1): 2.     
For more information see:
1 Brylinski M. (2013) eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures. BMC Res Notes 6 (1): 303.     
2 Brylinski M. (2013) The utility of artificially evolved sequences in protein threading and fold recognition. J Theor Biol 328: 77-88.     
For more information see:
1 Brylinski M, Feinstein WP. (2012) Setting up a meta-threading pipeline for high-throughput structural bioinformatics: eThread software distribution, walkthrough and resource profiling. J Comput Sci Syst Biol 6 (1): 001-010.    
2 Ragothaman A, Boddu SC, Kim N, Feinstein WP, Brylinski M, Jha S, Kim J. (2014) Developing eThread pipeline using SAGA-Pilot abstraction for large-scale structural bioinformatics. Biomed Res Int 2014: 348725.     
3 Feinstein WP, Brylinski M. (2015) Accelerated structural bioinformatics for drug discovery. High Performance Parallelism Pearls 2: 55-72.    
4 Feinstein WP, Moreno J, Jarrell M, Brylinski M. (2015) Accelerating the pace of protein functional annotation with Intel Xeon Phi coprocessors. IEEE Trans Nanobioscience 14 (4): 429-39.     
5 Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. (2016) GeauxDock: Accelerating structure-based virtual screening with heterogeneous computing. PLoS ONE 11 (7): e0158898.     
6 Feinstein WP, Brylinski M. (2016) Structure-based drug discovery accelerated by many-core devices. Curr Drug Targets 17 (14): 1595-609.     
For more information see:
1 Brylinski M. (2013) Unleashing the power of meta-threading for evolution/structure-based function inference of proteins. Front Genet 4: 118.     
2 Brylinski M, Feinstein WP. (2013) eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des 27 (6): 551-67.     
3 Feinstein WP, Brylinski M. (2014) eFindSite: Enhanced fingerprint-based virtual screening against predicted ligand binding sites in protein models. Mol Inf 33 (2): 135-50.     
For more information see:
1 Brylinski M. (2013) Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. Proteome Sci 11 (1): 47.     
For more information see:
1 Brylinski M. (2013) Nonlinear scoring functions for similarity-based ligand docking and binding affinity prediction. J Chem Inf Model 53 (11): 3097-112.     
For more information see:
1 Brylinski M, Waldrop GL. (2014) Computational redesign of bacterial biotin carboxylase inhibitors using structure-based virtual screening of combinatorial libraries. Molecules 19 (4): 4021-45.     
For more information see:
1 Brylinski M. (2014) eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 10 (9): e1003829.     
2 Brylinski M. (2017) Local alignment of ligand binding sites in proteins for polypharmacology and drug repositioning. Methods Mol Biol 1611: 109-22.     
3 Govindaraj RG, Brylinski M. (2018) Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 19 (1): 91.     
For more information see:
1 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Limbach PA, Bricker TM. (2014) Use of protein cross-linking and radiolytic footprinting to elucidate PsbP and PsbQ interactions within higher plant Photosystem II. Proc Natl Acad Sci USA 111 (45): 16178-83.     
2 Mummadisetti MP, Frankel LK, Bellamy HD, Sallans L, Goettert JS, Brylinski M, Bricker TM. (2016) Use of protein cross-linking and radiolytic labeling to elucidate the structure of PsbO within higher-plant photosystem II. Biochemistry 55 (23): 3204-13.     
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