BibTeX records: Eugene I. Shakhnovich

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@article{DBLP:journals/corr/abs-2012-07127,
  author       = {David E. Graff and
                  Eugene I. Shakhnovich and
                  Connor W. Coley},
  title        = {Accelerating high-throughput virtual screening through molecular pool-based
                  active learning},
  journal      = {CoRR},
  volume       = {abs/2012.07127},
  year         = {2020},
  url          = {https://arxiv.org/abs/2012.07127},
  eprinttype    = {arXiv},
  eprint       = {2012.07127},
  timestamp    = {Tue, 05 Jan 2021 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/corr/abs-2012-07127.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/RazbanGDSDCPS18,
  author       = {Rostam M. Razban and
                  Amy I Gilson and
                  Niamh Durfee and
                  Hendrik Strobelt and
                  Kasper Dinkla and
                  Jeong{-}Mo Choi and
                  Hanspeter Pfister and
                  Eugene I. Shakhnovich},
  title        = {ProteomeVis: a web app for exploration of protein properties from
                  structure to sequence evolution across organisms' proteomes},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {20},
  pages        = {3557--3565},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty370},
  doi          = {10.1093/BIOINFORMATICS/BTY370},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/RazbanGDSDCPS18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/RazbanGDSDCPS18a,
  author       = {Rostam M. Razban and
                  Amy I Gilson and
                  Niamh Durfee and
                  Hendrik Strobelt and
                  Kasper Dinkla and
                  Jeong{-}Mo Choi and
                  Hanspeter Pfister and
                  Eugene I. Shakhnovich},
  title        = {ProteomeVis: a web app for exploration of protein properties from
                  structure to sequence evolution across organisms' proteomes},
  journal      = {Bioinform.},
  volume       = {34},
  number       = {23},
  pages        = {4140},
  year         = {2018},
  url          = {https://doi.org/10.1093/bioinformatics/bty516},
  doi          = {10.1093/BIOINFORMATICS/BTY516},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/RazbanGDSDCPS18a.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcc/CheronS17,
  author       = {Nicolas Ch{\'{e}}ron and
                  Eugene I. Shakhnovich},
  title        = {Effect of sampling on {BACE-1} ligands binding free energy predictions
                  via {MM-PBSA} calculations},
  journal      = {J. Comput. Chem.},
  volume       = {38},
  number       = {22},
  pages        = {1941--1951},
  year         = {2017},
  url          = {https://doi.org/10.1002/jcc.24839},
  doi          = {10.1002/JCC.24839},
  timestamp    = {Wed, 01 Apr 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/jcc/CheronS17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/DebroiseSC17,
  author       = {Th{\'{e}}au Debroise and
                  Eugene I. Shakhnovich and
                  Nicolas Ch{\'{e}}ron},
  title        = {A Hybrid Knowledge-Based and Empirical Scoring Function for Protein-Ligand
                  Interaction: SMoG2016},
  journal      = {J. Chem. Inf. Model.},
  volume       = {57},
  number       = {3},
  pages        = {584--593},
  year         = {2017},
  url          = {https://doi.org/10.1021/acs.jcim.6b00610},
  doi          = {10.1021/ACS.JCIM.6B00610},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/DebroiseSC17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/JacquinGSCM16,
  author       = {Hugo Jacquin and
                  Amy Gilson and
                  Eugene I. Shakhnovich and
                  Simona Cocco and
                  R{\'{e}}mi Monasson},
  title        = {Benchmarking Inverse Statistical Approaches for Protein Structure
                  and Design with Exactly Solvable Models},
  journal      = {PLoS Comput. Biol.},
  volume       = {12},
  number       = {5},
  year         = {2016},
  url          = {https://doi.org/10.1371/journal.pcbi.1004889},
  doi          = {10.1371/JOURNAL.PCBI.1004889},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/JacquinGSCM16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/TianWWS15,
  author       = {Jian Tian and
                  Jaie C. Woodard and
                  Anna Whitney and
                  Eugene I. Shakhnovich},
  title        = {Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo
                  Unfolding Simulations and Its Functional Consequences},
  journal      = {PLoS Comput. Biol.},
  volume       = {11},
  number       = {4},
  year         = {2015},
  url          = {https://doi.org/10.1371/journal.pcbi.1004207},
  doi          = {10.1371/JOURNAL.PCBI.1004207},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/TianWWS15.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/EstacioKVMSF14,
  author       = {S{\'{\i}}lvia G. Est{\'{a}}cio and
                  Heinrich Krobath and
                  Diogo Vila{-}Vi{\c{c}}osa and
                  Miguel Machuqueiro and
                  Eugene I. Shakhnovich and
                  Patr{\'{\i}}cia F. N. Fa{\'{\i}}sca},
  title        = {A Simulated Intermediate State for Folding and Aggregation Provides
                  Insights into {\(\Delta\)}N6 {\(\beta\)}\({}_{\mbox{2}}\)-Microglobulin
                  Amyloidogenic Behavior},
  journal      = {PLoS Comput. Biol.},
  volume       = {10},
  number       = {5},
  year         = {2014},
  url          = {https://doi.org/10.1371/journal.pcbi.1003606},
  doi          = {10.1371/JOURNAL.PCBI.1003606},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/EstacioKVMSF14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/DasmehSKS13,
  author       = {Pouria Dasmeh and
                  Adrian W. R. Serohijos and
                  Kasper P. Kepp and
                  Eugene I. Shakhnovich},
  title        = {Positively Selected Sites in Cetacean Myoglobins Contribute to Protein
                  Stability},
  journal      = {PLoS Comput. Biol.},
  volume       = {9},
  number       = {3},
  year         = {2013},
  url          = {https://doi.org/10.1371/journal.pcbi.1002929},
  doi          = {10.1371/JOURNAL.PCBI.1002929},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/DasmehSKS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/CetinbasS13,
  author       = {Murat {\c{C}}etinbas and
                  Eugene I. Shakhnovich},
  title        = {Catalysis of Protein Folding by Chaperones Accelerates Evolutionary
                  Dynamics in Adapting Cell Populations},
  journal      = {PLoS Comput. Biol.},
  volume       = {9},
  number       = {11},
  year         = {2013},
  url          = {https://doi.org/10.1371/journal.pcbi.1003269},
  doi          = {10.1371/JOURNAL.PCBI.1003269},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/CetinbasS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/WylieS12,
  author       = {C. Scott Wylie and
                  Eugene I. Shakhnovich},
  title        = {Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis
                  and Lethal Isolation},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {8},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002609},
  doi          = {10.1371/JOURNAL.PCBI.1002609},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/WylieS12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/MannigeBS12,
  author       = {Ranjan V. Mannige and
                  Charles L. Brooks III and
                  Eugene I. Shakhnovich},
  title        = {A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor},
  journal      = {PLoS Comput. Biol.},
  volume       = {8},
  number       = {12},
  year         = {2012},
  url          = {https://doi.org/10.1371/journal.pcbi.1002839},
  doi          = {10.1371/JOURNAL.PCBI.1002839},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/MannigeBS12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/HeoS10,
  author       = {Muyoung Heo and
                  Eugene I. Shakhnovich},
  title        = {Interplay between Pleiotropy and Secondary Selection Determines Rise
                  and Fall of Mutators in Stress Response},
  journal      = {PLoS Comput. Biol.},
  volume       = {6},
  number       = {3},
  year         = {2010},
  url          = {https://doi.org/10.1371/journal.pcbi.1000710},
  doi          = {10.1371/JOURNAL.PCBI.1000710},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/HeoS10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/ZhangS10,
  author       = {Jingshan Zhang and
                  Eugene I. Shakhnovich},
  title        = {Optimality of Mutation and Selection in Germinal Centers},
  journal      = {PLoS Comput. Biol.},
  volume       = {6},
  number       = {6},
  year         = {2010},
  url          = {https://doi.org/10.1371/journal.pcbi.1000800},
  doi          = {10.1371/JOURNAL.PCBI.1000800},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/ZhangS10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcb/LeeZS09,
  author       = {J. William Lee and
                  Tomasz Zemojtel and
                  Eugene I. Shakhnovich},
  title        = {Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein
                  Complexes},
  journal      = {J. Comput. Biol.},
  volume       = {16},
  number       = {2},
  pages        = {331--339},
  year         = {2009},
  url          = {https://doi.org/10.1089/cmb.2008.17TT},
  doi          = {10.1089/CMB.2008.17TT},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcb/LeeZS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/jcisd/KutchukianLS09,
  author       = {Peter S. Kutchukian and
                  David Lou and
                  Eugene I. Shakhnovich},
  title        = {{FOG:} Fragment Optimized Growth Algorithm for the \emph{de Novo}
                  Generation of Molecules Occupying Druglike Chemical Space},
  journal      = {J. Chem. Inf. Model.},
  volume       = {49},
  number       = {7},
  pages        = {1630--1642},
  year         = {2009},
  url          = {https://doi.org/10.1021/ci9000458},
  doi          = {10.1021/CI9000458},
  timestamp    = {Fri, 06 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/jcisd/KutchukianLS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/nar/DonaldS09,
  author       = {Jason E. Donald and
                  Eugene I. Shakhnovich},
  title        = {{SDR:} a database of predicted specificity-determining residues in
                  proteins},
  journal      = {Nucleic Acids Res.},
  volume       = {37},
  number       = {Database-Issue},
  pages        = {191--194},
  year         = {2009},
  url          = {https://doi.org/10.1093/nar/gkn716},
  doi          = {10.1093/NAR/GKN716},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/DonaldS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/ZeldovichBS07,
  author       = {Konstantin B. Zeldovich and
                  Igor N. Berezovsky and
                  Eugene I. Shakhnovich},
  title        = {Protein and {DNA} Sequence Determinants of Thermophilic Adaptation},
  journal      = {PLoS Comput. Biol.},
  volume       = {3},
  number       = {1},
  year         = {2007},
  url          = {https://doi.org/10.1371/journal.pcbi.0030005},
  doi          = {10.1371/JOURNAL.PCBI.0030005},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/ZeldovichBS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/BerezovskyZS07,
  author       = {Igor N. Berezovsky and
                  Konstantin B. Zeldovich and
                  Eugene I. Shakhnovich},
  title        = {Positive and Negative Design in Stability and Thermal Adaptation of
                  Natural Proteins},
  journal      = {PLoS Comput. Biol.},
  volume       = {3},
  number       = {3},
  year         = {2007},
  url          = {https://doi.org/10.1371/journal.pcbi.0030052},
  doi          = {10.1371/JOURNAL.PCBI.0030052},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/BerezovskyZS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/ZeldovichCSS07,
  author       = {Konstantin B. Zeldovich and
                  Peiqiu Chen and
                  Boris E. Shakhnovich and
                  Eugene I. Shakhnovich},
  title        = {A First-Principles Model of Early Evolution: Emergence of Gene Families,
                  Species, and Preferred Protein Folds},
  journal      = {PLoS Comput. Biol.},
  volume       = {3},
  number       = {7},
  year         = {2007},
  url          = {https://doi.org/10.1371/journal.pcbi.0030139},
  doi          = {10.1371/JOURNAL.PCBI.0030139},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/ZeldovichCSS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/GrotthussPGRS06,
  author       = {Marcin von Grotthuss and
                  Dariusz Plewczynski and
                  Krzysztof Ginalski and
                  Leszek Rychlewski and
                  Eugene I. Shakhnovich},
  title        = {{PDB-UF:} database of predicted enzymatic functions for unannotated
                  protein structures from structural genomics},
  journal      = {{BMC} Bioinform.},
  volume       = {7},
  pages        = {53},
  year         = {2006},
  url          = {https://doi.org/10.1186/1471-2105-7-53},
  doi          = {10.1186/1471-2105-7-53},
  timestamp    = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/GrotthussPGRS06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/DonaldHRSM05,
  author       = {Jason E. Donald and
                  Isaac A. Hubner and
                  Veronica Rotemberg and
                  Eugene I. Shakhnovich and
                  Leonid A. Mirny},
  title        = {CoC: a database of universally conserved residues in protein folds},
  journal      = {Bioinform.},
  volume       = {21},
  number       = {10},
  pages        = {2539--2540},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti360},
  doi          = {10.1093/BIOINFORMATICS/BTI360},
  timestamp    = {Sat, 30 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DonaldHRSM05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bioinformatics/DonaldS05,
  author       = {Jason E. Donald and
                  Eugene I. Shakhnovich},
  title        = {Determining functional specificity from protein sequences},
  journal      = {Bioinform.},
  volume       = {21},
  number       = {11},
  pages        = {2629--2635},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti396},
  doi          = {10.1093/BIOINFORMATICS/BTI396},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/DonaldS05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/ploscb/BerezovskyCCS05,
  author       = {Igor N. Berezovsky and
                  William W. Chen and
                  Paul J. Choi and
                  Eugene I. Shakhnovich},
  title        = {Entropic Stabilization of Proteins and Its Proteomic Consequences},
  journal      = {PLoS Comput. Biol.},
  volume       = {1},
  number       = {4},
  year         = {2005},
  url          = {https://doi.org/10.1371/journal.pcbi.0010047},
  doi          = {10.1371/JOURNAL.PCBI.0010047},
  timestamp    = {Thu, 10 Sep 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/ploscb/BerezovskyCCS05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@article{DBLP:journals/bmcbi/ShakhnovichHCLDS03,
  author       = {Boris E. Shakhnovich and
                  John M. Harvey and
                  Steve Comeau and
                  David Lorenz and
                  Charles DeLisi and
                  Eugene I. Shakhnovich},
  title        = {{ELISA:} Structure-Function Inferences based on statistically significant
                  and evolutionarily inspired observations},
  journal      = {{BMC} Bioinform.},
  volume       = {4},
  pages        = {34},
  year         = {2003},
  url          = {https://doi.org/10.1186/1471-2105-4-34},
  doi          = {10.1186/1471-2105-4-34},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcbi/ShakhnovichHCLDS03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/psb/KissingerDS99,
  author       = {C. Kissinger and
                  A. Keith Dunker and
                  Eugene I. Shakhnovich},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Teri E. Klein},
  title        = {Disorder in Protein Structure and Function - Session Introduction},
  booktitle    = {Proceedings of the 4th Pacific Symposium on Biocomputing, {PSB} 1999,
                  The Orchid at Mauna Lani, Big Island of Hawaii, USA, January 4-9,
                  1999},
  pages        = {517--519},
  year         = {1999},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb99/Disorder.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/KissingerDS99.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

@inproceedings{DBLP:conf/dimacs/SaliSK95,
  author       = {Andrej Sali and
                  Eugene I. Shakhnovich and
                  Martin Karplus},
  editor       = {Panos M. Pardalos and
                  David Shalloway and
                  Guoliang Xue},
  title        = {Thermodynamics and kinetics of protein folding},
  booktitle    = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation
                  and Protein Folding, Proceedings of a {DIMACS} Workshop, USA, March
                  20-21, 1995},
  series       = {{DIMACS} Series in Discrete Mathematics and Theoretical Computer Science},
  volume       = {23},
  pages        = {199--213},
  publisher    = {{DIMACS/AMS}},
  year         = {1995},
  url          = {https://doi.org/10.1090/dimacs/023/13},
  doi          = {10.1090/DIMACS/023/13},
  timestamp    = {Mon, 22 May 2023 16:07:35 +0200},
  biburl       = {https://dblp.org/rec/conf/dimacs/SaliSK95.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}

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