Michal Brylinski

Publication Activity (10 Years)

Years Active: 2004-2022
Publications (10 Years): 14

Top Topics

Virtual Screening

Scoring Function

Top Venues

J. Cheminformatics

Briefings Bioinform.

Publications

Supratik Mukhopadhyay, Michal Brylinski, Adam Bess, Frej Berglind, Chris Galliano, Patrick F. McGrew
DeepDrug: Applying AI for the Advancement of Drug Discovery. COMSNETS (2022)
Guannan Liu, Manali Singha, Limeng Pu, Prasanga Neupane, Joseph Feinstein, Hsiao-Chun Wu, J. Ramanujam, Michal Brylinski
GraphDTI: A robust deep learning predictor of drug-target interactions from multiple heterogeneous data. J. Cheminformatics 13 (1) (2021)
Wentao Shi, Jeffrey Mitchell Lemoine, Abd-El-Monsif A. Shawky, Manali Singha, Limeng Pu, Shuangyan Yang, J. Ramanujam, Michal Brylinski
BionoiNet: ligand-binding site classification with off-the-shelf deep neural network. Bioinform. 36 (10) (2020)
Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski
DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput. Biol. 15 (2) (2019)
Eroma Abeysinghe, Michal Brylinski, Marcus Christie, Suresh Marru, Marlon E. Pierce
LSU Computational System Biology Gateway for Education. PEARC (2019)
Misagh Naderi, Jeffrey Mitchell Lemoine, Rajiv Gandhi Govindaraj, Omar Kana, Wei Pan Feinstein, Michal Brylinski
Binding site matching in rational drug design: algorithms and applications. Briefings Bioinform. 20 (6) (2019)
Omar Kana, Michal Brylinski
Elucidating the druggability of the human proteome with eFindSite. J. Comput. Aided Mol. Des. 33 (5) (2019)
Eroma Abeysinghe, Michal Brylinski, Marcus Christie, Suresh Marru, Marlon E. Pierce
The CSBG - LSU Gateway: Web based Hosted Gateway for Computational System Biology Application Tools from Louisiana State University. PEARC (2018)
Rajiv Gandhi Govindaraj, Michal Brylinski
Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinform. 19 (1) (2018)
Surabhi Maheshwari, Michal Brylinski
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. BMC Bioinform. 18 (1) (2017)
Tairan Liu, Misagh Naderi, Chris Alvin, Supratik Mukhopadhyay, Michal Brylinski
MolFrag. J. Chem. Inf. Model. 57 (4) (2017)
Misagh Naderi, Chris Alvin, Yun Ding, Supratik Mukhopadhyay, Michal Brylinski
A graph-based approach to construct target-focused libraries for virtual screening. J. Cheminformatics 8 (1) (2016)
Chen Wang, Gang Hu, Kui Wang, Michal Brylinski, Lei Xie, Lukasz A. Kurgan
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinform. 32 (4) (2016)
Yun Ding, Ye Fang, Juana Moreno, J. Ramanujam, Mark Jarrell, Michal Brylinski
Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput. Biol. Chem. 64 (2016)
Surabhi Maheshwari, Michal Brylinski
Predicting protein interface residues using easily accessible on-line resources. Briefings Bioinform. 16 (6) (2015)
Michal Brylinski
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) (2015)
Yun Ding, Ye Fang, Wei Pan Feinstein, Jagannathan Ramanujam, David M. Koppelman, Juana Moreno, Michal Brylinski, Mark Jarrell
GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J. Comput. Chem. 36 (27) (2015)
Wei Pan Feinstein, Michal Brylinski
Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. J. Cheminformatics 7 (2015)
Michal Brylinski
MatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models. PLoS Comput. Biol. 10 (9) (2014)
Michal Brylinski
Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction. J. Chem. Inf. Model. 53 (11) (2013)
Michal Brylinski, Wei Pan Feinstein
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) (2013)
Michal Brylinski, Jeffrey Skolnick
: Low-resolution refinement for ligand comparative modeling. J. Comput. Chem. 31 (5) (2010)
Shashi Bhushan Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, Jeffrey Skolnick
PSiFR: an integrated resource for prediction of protein structure and function. Bioinform. 26 (5) (2010)
Michal Brylinski, Jeffrey Skolnick
Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. J. Chem. Inf. Model. 50 (10) (2010)
Jeffrey Skolnick, Michal Brylinski
FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings Bioinform. 10 (4) (2009)
Michal Brylinski, Jeffrey Skolnick
: A Threading-Based Approach to Ligand Homology Modeling. PLoS Comput. Biol. 5 (6) (2009)
Michal Brylinski, Jeffrey Skolnick
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J. Comput. Chem. 29 (10) (2008)
Michal Brylinski, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochanczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman
Prediction of Functional Sites Based on the Fuzzy Oil Drop Model. PLoS Comput. Biol. 3 (5) (2007)
Michal Brylinski, Leszek Konieczny, Irena Roterman
Is the protein folding an aim-oriented process? Human haemoglobin as example. Int. J. Bioinform. Res. Appl. 3 (2) (2007)
Michal Brylinski, Leszek Konieczny, Irena Roterman
) protein folding. Comput. Biol. Chem. 30 (4) (2006)
Leszek Konieczny, Michal Brylinski, Irena Roterman
Gauss-Function-Based Model of Hydrophobicity Density in Proteins. Silico Biol. 6 (1-2) (2006)
Michal Brylinski, Marek Kochanczyk, Leszek Konieczny, Irena Roterman
Sequence-Structure-Function Relation Characterized in silico. Silico Biol. 6 (6) (2006)
Michal Brylinski, Wiktor Jurkowski, Leszek Konieczny, Irena Roterman
Limited conformational space for early-stage protein folding simulation. Bioinform. 20 (2) (2004)
Michal Brylinski, Leszek Konieczny, Irena Roterman
SPI - Structure predictability index for protein sequences. Silico Biol. 5 (3) (2004)