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BibTeX records: Michal Brylinski
@inproceedings{DBLP:conf/comsnets/MukhopadhyayBBB22, author = {Supratik Mukhopadhyay and Michal Brylinski and Adam Bess and Frej Berglind and Chris Galliano and Patrick F. McGrew}, title = {DeepDrug: Applying {AI} for the Advancement of Drug Discovery}, booktitle = {14th International Conference on COMmunication Systems {\&} NETworkS, {COMSNETS} 2022, Bangalore, India, January 4-8, 2022}, pages = {667--674}, publisher = {{IEEE}}, year = {2022}, url = {https://doi.org/10.1109/COMSNETS53615.2022.9668586}, doi = {10.1109/COMSNETS53615.2022.9668586}, timestamp = {Tue, 25 Jan 2022 16:35:12 +0100}, biburl = {https://dblp.org/rec/conf/comsnets/MukhopadhyayBBB22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/LiuSPNFWRB21, author = {Guannan Liu and Manali Singha and Limeng Pu and Prasanga Neupane and Joseph Feinstein and Hsiao{-}Chun Wu and J. Ramanujam and Michal Brylinski}, title = {GraphDTI: {A} robust deep learning predictor of drug-target interactions from multiple heterogeneous data}, journal = {J. Cheminformatics}, volume = {13}, number = {1}, pages = {58}, year = {2021}, url = {https://doi.org/10.1186/s13321-021-00540-0}, doi = {10.1186/S13321-021-00540-0}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcheminf/LiuSPNFWRB21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ShiLSSPYRB20, author = {Wentao Shi and Jeffrey Mitchell Lemoine and Abd{-}El{-}Monsif A. Shawky and Manali Singha and Limeng Pu and Shuangyan Yang and J. Ramanujam and Michal Brylinski}, title = {BionoiNet: ligand-binding site classification with off-the-shelf deep neural network}, journal = {Bioinform.}, volume = {36}, number = {10}, pages = {3077--3083}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btaa094}, doi = {10.1093/BIOINFORMATICS/BTAA094}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/ShiLSSPYRB20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/NaderiLGKFB19, author = {Misagh Naderi and Jeffrey Mitchell Lemoine and Rajiv Gandhi Govindaraj and Omar Kana and Wei Pan Feinstein and Michal Brylinski}, title = {Binding site matching in rational drug design: algorithms and applications}, journal = {Briefings Bioinform.}, volume = {20}, number = {6}, pages = {2167--2184}, year = {2019}, url = {https://doi.org/10.1093/bib/bby078}, doi = {10.1093/BIB/BBY078}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/NaderiLGKFB19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/KanaB19, author = {Omar Kana and Michal Brylinski}, title = {Elucidating the druggability of the human proteome with eFindSite}, journal = {J. Comput. Aided Mol. Des.}, volume = {33}, number = {5}, pages = {509--519}, year = {2019}, url = {https://doi.org/10.1007/s10822-019-00197-w}, doi = {10.1007/S10822-019-00197-W}, timestamp = {Sat, 30 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/KanaB19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/PuGLWB19, author = {Limeng Pu and Rajiv Gandhi Govindaraj and Jeffrey Mitchell Lemoine and Hsiao{-}Chun Wu and Michal Brylinski}, title = {DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network}, journal = {PLoS Comput. Biol.}, volume = {15}, number = {2}, year = {2019}, url = {https://doi.org/10.1371/journal.pcbi.1006718}, doi = {10.1371/JOURNAL.PCBI.1006718}, timestamp = {Sat, 25 Dec 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/ploscb/PuGLWB19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/xsede/AbeysingheBCMP19, author = {Eroma Abeysinghe and Michal Brylinski and Marcus Christie and Suresh Marru and Marlon E. Pierce}, editor = {Thomas R. Furlani}, title = {{LSU} Computational System Biology Gateway for Education}, booktitle = {Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), {PEARC} 2019, Chicago, IL, USA, July 28 - August 01, 2019}, pages = {112:1--112:4}, publisher = {{ACM}}, year = {2019}, url = {https://doi.org/10.1145/3332186.3333259}, doi = {10.1145/3332186.3333259}, timestamp = {Mon, 03 Jan 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/xsede/AbeysingheBCMP19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/GovindarajB18, author = {Rajiv Gandhi Govindaraj and Michal Brylinski}, title = {Comparative assessment of strategies to identify similar ligand-binding pockets in proteins}, journal = {{BMC} Bioinform.}, volume = {19}, number = {1}, pages = {91:1--91:17}, year = {2018}, url = {https://doi.org/10.1186/s12859-018-2109-2}, doi = {10.1186/S12859-018-2109-2}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/GovindarajB18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/xsede/AbeysingheBCMP18, author = {Eroma Abeysinghe and Michal Brylinski and Marcus Christie and Suresh Marru and Marlon E. Pierce}, editor = {Sergiu Sanielevici}, title = {The {CSBG} - {LSU} Gateway: Web based Hosted Gateway for Computational System Biology Application Tools from Louisiana State University}, booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing, {PEARC} 2018, Pittsburgh, PA, USA, July 22-26, 2018}, pages = {100:1--100:4}, publisher = {{ACM}}, year = {2018}, url = {https://doi.org/10.1145/3219104.3229245}, doi = {10.1145/3219104.3229245}, timestamp = {Wed, 25 Sep 2019 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/xsede/AbeysingheBCMP18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/MaheshwariB17, author = {Surabhi Maheshwari and Michal Brylinski}, title = {Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks}, journal = {{BMC} Bioinform.}, volume = {18}, number = {1}, pages = {257:1--257:14}, year = {2017}, url = {https://doi.org/10.1186/s12859-017-1675-z}, doi = {10.1186/S12859-017-1675-Z}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/MaheshwariB17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcisd/LiuNAMB17, author = {Tairan Liu and Misagh Naderi and Chris Alvin and Supratik Mukhopadhyay and Michal Brylinski}, title = {Break Down in Order To Build Up: Decomposing Small Molecules for Fragment-Based Drug Design with \emph{e}MolFrag}, journal = {J. Chem. Inf. Model.}, volume = {57}, number = {4}, pages = {627--631}, year = {2017}, url = {https://doi.org/10.1021/acs.jcim.6b00596}, doi = {10.1021/ACS.JCIM.6B00596}, timestamp = {Fri, 06 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcisd/LiuNAMB17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/WangHWBXK16, author = {Chen Wang and Gang Hu and Kui Wang and Michal Brylinski and Lei Xie and Lukasz A. Kurgan}, title = {{PDID:} database of molecular-level putative protein-drug interactions in the structural human proteome}, journal = {Bioinform.}, volume = {32}, number = {4}, pages = {579--586}, year = {2016}, url = {https://doi.org/10.1093/bioinformatics/btv597}, doi = {10.1093/BIOINFORMATICS/BTV597}, timestamp = {Thu, 14 Oct 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/WangHWBXK16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/candc/DingFMRJB16, author = {Yun Ding and Ye Fang and Juana Moreno and J. Ramanujam and Mark Jarrell and Michal Brylinski}, title = {Assessing the similarity of ligand binding conformations with the Contact Mode Score}, journal = {Comput. Biol. Chem.}, volume = {64}, pages = {403--413}, year = {2016}, url = {https://doi.org/10.1016/j.compbiolchem.2016.08.007}, doi = {10.1016/J.COMPBIOLCHEM.2016.08.007}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/candc/DingFMRJB16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/NaderiADMB16, author = {Misagh Naderi and Chris Alvin and Yun Ding and Supratik Mukhopadhyay and Michal Brylinski}, title = {A graph-based approach to construct target-focused libraries for virtual screening}, journal = {J. Cheminformatics}, volume = {8}, number = {1}, pages = {14:1--14:16}, year = {2016}, url = {https://doi.org/10.1186/s13321-016-0126-6}, doi = {10.1186/S13321-016-0126-6}, timestamp = {Wed, 14 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcheminf/NaderiADMB16.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bams/Brylinski15, author = {Michal Brylinski}, title = {Is the growth rate of Protein Data Bank sufficient to solve the protein structure prediction problem using template-based modeling?}, journal = {Bio Algorithms Med Syst.}, volume = {11}, number = {1}, pages = {1--7}, year = {2015}, url = {https://doi.org/10.1515/bams-2014-0024}, doi = {10.1515/BAMS-2014-0024}, timestamp = {Thu, 20 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bams/Brylinski15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MaheshwariB15, author = {Surabhi Maheshwari and Michal Brylinski}, title = {Predicting protein interface residues using easily accessible on-line resources}, journal = {Briefings Bioinform.}, volume = {16}, number = {6}, pages = {1025--1034}, year = {2015}, url = {https://doi.org/10.1093/bib/bbv009}, doi = {10.1093/BIB/BBV009}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MaheshwariB15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcc/DingFFRKMBJ15, author = {Yun Ding and Ye Fang and Wei Pan Feinstein and Jagannathan Ramanujam and David M. Koppelman and Juana Moreno and Michal Brylinski and Mark Jarrell}, title = {GeauxDock: {A} novel approach for mixed-resolution ligand docking using a descriptor-based force field}, journal = {J. Comput. Chem.}, volume = {36}, number = {27}, pages = {2013--2026}, year = {2015}, url = {https://doi.org/10.1002/jcc.24031}, doi = {10.1002/JCC.24031}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcc/DingFFRKMBJ15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcheminf/FeinsteinB15, author = {Wei Pan Feinstein and Michal Brylinski}, title = {Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets}, journal = {J. Cheminformatics}, volume = {7}, pages = {18:1--18:10}, year = {2015}, url = {https://doi.org/10.1186/s13321-015-0067-5}, doi = {10.1186/S13321-015-0067-5}, timestamp = {Fri, 07 Feb 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcheminf/FeinsteinB15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/Brylinski14, author = {Michal Brylinski}, title = {\emph{e}MatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models}, journal = {PLoS Comput. Biol.}, volume = {10}, number = {9}, year = {2014}, url = {https://doi.org/10.1371/journal.pcbi.1003829}, doi = {10.1371/JOURNAL.PCBI.1003829}, timestamp = {Mon, 26 Sep 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/Brylinski14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcamd/BrylinskiF13, author = {Michal Brylinski and Wei Pan Feinstein}, title = {eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands}, journal = {J. Comput. Aided Mol. Des.}, volume = {27}, number = {6}, pages = {551--567}, year = {2013}, url = {https://doi.org/10.1007/s10822-013-9663-5}, doi = {10.1007/S10822-013-9663-5}, timestamp = {Thu, 16 Apr 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcamd/BrylinskiF13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcisd/Brylinski13, author = {Michal Brylinski}, title = {Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction}, journal = {J. Chem. Inf. Model.}, volume = {53}, number = {11}, pages = {3097--3112}, year = {2013}, url = {https://doi.org/10.1021/ci400510e}, doi = {10.1021/CI400510E}, timestamp = {Fri, 06 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcisd/Brylinski13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PanditBZGAS10, author = {Shashi Bhushan Pandit and Michal Brylinski and Hongyi Zhou and Mu Gao and Adrian K. Arakaki and Jeffrey Skolnick}, title = {PSiFR: an integrated resource for prediction of protein structure and function}, journal = {Bioinform.}, volume = {26}, number = {5}, pages = {687--688}, year = {2010}, url = {https://doi.org/10.1093/bioinformatics/btq006}, doi = {10.1093/BIOINFORMATICS/BTQ006}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/PanditBZGAS10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcc/BrylinskiS10, author = {Michal Brylinski and Jeffrey Skolnick}, title = {Q-Dock\({}^{\mbox{LHM}}\): Low-resolution refinement for ligand comparative modeling}, journal = {J. Comput. Chem.}, volume = {31}, number = {5}, pages = {1093--1105}, year = {2010}, url = {https://doi.org/10.1002/jcc.21395}, doi = {10.1002/JCC.21395}, timestamp = {Wed, 01 Apr 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcc/BrylinskiS10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcisd/BrylinskiS10, author = {Michal Brylinski and Jeffrey Skolnick}, title = {Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening}, journal = {J. Chem. Inf. Model.}, volume = {50}, number = {10}, pages = {1839--1854}, year = {2010}, url = {https://doi.org/10.1021/ci100235n}, doi = {10.1021/CI100235N}, timestamp = {Fri, 06 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcisd/BrylinskiS10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SkolnickB09, author = {Jeffrey Skolnick and Michal Brylinski}, title = {{FINDSITE:} a combined evolution/structure-based approach to protein function prediction}, journal = {Briefings Bioinform.}, volume = {10}, number = {4}, pages = {378--391}, year = {2009}, url = {https://doi.org/10.1093/bib/bbp017}, doi = {10.1093/BIB/BBP017}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SkolnickB09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/BrylinskiS09, author = {Michal Brylinski and Jeffrey Skolnick}, title = {FINDSITE\({}^{\mbox{LHM}}\): {A} Threading-Based Approach to Ligand Homology Modeling}, journal = {PLoS Comput. Biol.}, volume = {5}, number = {6}, year = {2009}, url = {https://doi.org/10.1371/journal.pcbi.1000405}, doi = {10.1371/JOURNAL.PCBI.1000405}, timestamp = {Thu, 10 Sep 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/BrylinskiS09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcc/BrylinskiS08, author = {Michal Brylinski and Jeffrey Skolnick}, title = {Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints}, journal = {J. Comput. Chem.}, volume = {29}, number = {10}, pages = {1574--1588}, year = {2008}, url = {https://doi.org/10.1002/jcc.20917}, doi = {10.1002/JCC.20917}, timestamp = {Wed, 01 Apr 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcc/BrylinskiS08.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ijbra/BrylinskiKR07, author = {Michal Brylinski and Leszek Konieczny and Irena Roterman}, title = {Is the protein folding an aim-oriented process? Human haemoglobin as example}, journal = {Int. J. Bioinform. Res. Appl.}, volume = {3}, number = {2}, pages = {234--260}, year = {2007}, url = {https://doi.org/10.1504/IJBRA.2007.013605}, doi = {10.1504/IJBRA.2007.013605}, timestamp = {Fri, 11 Sep 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ijbra/BrylinskiKR07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ploscb/BrylinskiPJKSKR07, author = {Michal Brylinski and Katarzyna Prymula and Wiktor Jurkowski and Marek Kochanczyk and Ewa Stawowczyk and Leszek Konieczny and Irena Roterman}, title = {Prediction of Functional Sites Based on the Fuzzy Oil Drop Model}, journal = {PLoS Comput. Biol.}, volume = {3}, number = {5}, year = {2007}, url = {https://doi.org/10.1371/journal.pcbi.0030094}, doi = {10.1371/JOURNAL.PCBI.0030094}, timestamp = {Thu, 10 Sep 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/ploscb/BrylinskiPJKSKR07.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/candc/BrylinskiKR06, author = {Michal Brylinski and Leszek Konieczny and Irena Roterman}, title = {Hydrophobic collapse in (\emph{in silico}) protein folding}, journal = {Comput. Biol. Chem.}, volume = {30}, number = {4}, pages = {255--267}, year = {2006}, url = {https://doi.org/10.1016/j.compbiolchem.2006.04.007}, doi = {10.1016/J.COMPBIOLCHEM.2006.04.007}, timestamp = {Fri, 13 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/candc/BrylinskiKR06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/isb/KoniecznyBR06, author = {Leszek Konieczny and Michal Brylinski and Irena Roterman}, title = {Gauss-Function-Based Model of Hydrophobicity Density in Proteins}, journal = {Silico Biol.}, volume = {6}, number = {1-2}, pages = {15--22}, year = {2006}, url = {http://content.iospress.com/articles/in-silico-biology/isb00217}, timestamp = {Thu, 20 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/isb/KoniecznyBR06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/isb/BrylinskiKKR06, author = {Michal Brylinski and Marek Kochanczyk and Leszek Konieczny and Irena Roterman}, title = {Sequence-Structure-Function Relation Characterized in silico}, journal = {Silico Biol.}, volume = {6}, number = {6}, pages = {589--600}, year = {2006}, url = {http://content.iospress.com/articles/in-silico-biology/isb00267}, timestamp = {Thu, 20 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/isb/BrylinskiKKR06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/BrylinskiJKR04, author = {Michal Brylinski and Wiktor Jurkowski and Leszek Konieczny and Irena Roterman}, title = {Limited conformational space for early-stage protein folding simulation}, journal = {Bioinform.}, volume = {20}, number = {2}, pages = {199--205}, year = {2004}, url = {https://doi.org/10.1093/bioinformatics/btg391}, doi = {10.1093/BIOINFORMATICS/BTG391}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/BrylinskiJKR04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/isb/BrylinskiKR04, author = {Michal Brylinski and Leszek Konieczny and Irena Roterman}, title = {{SPI} - Structure predictability index for protein sequences}, journal = {Silico Biol.}, volume = {5}, number = {3}, pages = {227--237}, year = {2004}, url = {http://content.iospress.com/articles/in-silico-biology/isb00182}, timestamp = {Thu, 20 Aug 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/isb/BrylinskiKR04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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