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ORCIDBibTeX records: Ruben Abagyan
@article{DBLP:journals/jcisd/RaushAT22,
author = {Eugene Raush and
Ruben Abagyan and
Maxim Totrov},
title = {Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles
for Small Organic Molecules},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {23},
pages = {5896--5906},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00790},
doi = {10.1021/ACS.JCIM.2C00790},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/RaushAT22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RosenthalWSLAMC22,
author = {Sara Brin Rosenthal and
Hao Wang and
Da Shi and
Cin Liu and
Ruben Abagyan and
Linda K. McEvoy and
Chi{-}Hua Chen},
title = {Mapping the gene network landscape of Alzheimer's disease through
integrating genomics and transcriptomics},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {2},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1009903},
doi = {10.1371/JOURNAL.PCBI.1009903},
timestamp = {Mon, 15 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RosenthalWSLAMC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/XiongJAKPLJKJZT21,
author = {Zhaoping Xiong and
Minji Jeon and
Robert J. Allaway and
Jaewoo Kang and
Donghyeon Park and
Jinhyuk Lee and
Hwisang Jeon and
Miyoung Ko and
Hualiang Jiang and
Mingyue Zheng and
Aik Choon Tan and
Xindi Guo and
Multi{-}Targeting Drug DREAM Challenge Community and
Kristen K. Dang and
Alex Tropsha and
Chana Hecht and
Tirtha K. Das and
Heather A. Carlson and
Ruben Abagyan and
Justin Guinney and
Avner Schlessinger and
Ross L. Cagan},
title = {Crowdsourced identification of multi-target kinase inhibitors for
{RET-} and {TAU-} based disease: The Multi-Targeting Drug {DREAM}
Challenge},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {9},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009302},
doi = {10.1371/JOURNAL.PCBI.1009302},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/XiongJAKPLJKJZT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NicolaKIA20,
author = {George Nicola and
Irina Kufareva and
Andrey V. Ilatovskiy and
Ruben Abagyan},
title = {Druggable exosites of the human kino-pocketome},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {3},
pages = {219--230},
year = {2020},
url = {https://doi.org/10.1007/s10822-019-00276-y},
doi = {10.1007/S10822-019-00276-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NicolaKIA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT19,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Hybrid receptor structure/ligand-based docking and activity prediction
in {ICM:} development and evaluation in {D3R} Grand Challenge 3},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {1},
pages = {35--46},
year = {2019},
url = {https://doi.org/10.1007/s10822-018-0139-5},
doi = {10.1007/S10822-018-0139-5},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT19a,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Macrocycle modeling in {ICM:} benchmarking and evaluation in {D3R}
Grand Challenge 4},
journal = {J. Comput. Aided Mol. Des.},
volume = {33},
number = {12},
pages = {1057--1069},
year = {2019},
url = {https://doi.org/10.1007/s10822-019-00225-9},
doi = {10.1007/S10822-019-00225-9},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT19a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ShiKA19,
author = {Da Shi and
Feroz Khan and
Ruben Abagyan},
title = {Extended Multitarget Pharmacology of Anticancer Drugs},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {6},
pages = {3006--3017},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00031},
doi = {10.1021/ACS.JCIM.9B00031},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ShiKA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/LamAT18,
author = {Polo Chun{-}Hung Lam and
Ruben Abagyan and
Maxim Totrov},
title = {Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor
structure-based approach},
journal = {J. Comput. Aided Mol. Des.},
volume = {32},
number = {1},
pages = {187--198},
year = {2018},
url = {https://doi.org/10.1007/s10822-017-0058-x},
doi = {10.1007/S10822-017-0058-X},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/LamAT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WarszyckiRMKSRC17,
author = {Dawid Warszycki and
Manuel Rueda and
Stefan Mordalski and
Kurt Kristiansen and
Grzegorz Satala and
Krzysztof Rataj and
Zdzislaw Chilmonczyk and
Ingebrigt Sylte and
Ruben Abagyan and
Andrzej J. Bojarski},
title = {From Homology Models to a Set of Predictive Binding Pockets-a 5-HT\({}_{\mbox{1A}}\)
Receptor Case Study},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {2},
pages = {311--321},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.6b00263},
doi = {10.1021/ACS.JCIM.6B00263},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/WarszyckiRMKSRC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/GeidlBRVHKAK15,
author = {Stanislav Geidl and
Tom{\'{a}}s Bouchal and
Tom{\'{a}}s Racek and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
V{\'{a}}clav Hejret and
Ales Krenek and
Ruben Abagyan and
Jaroslav Koca},
title = {High-quality and universal empirical atomic charges for chemoinformatics
applications},
journal = {J. Cheminformatics},
volume = {7},
pages = {59:1--59:10},
year = {2015},
url = {https://doi.org/10.1186/s13321-015-0107-1},
doi = {10.1186/S13321-015-0107-1},
timestamp = {Thu, 23 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/GeidlBRVHKAK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/StieflGCHLSSBBK15,
author = {Nikolaus Stiefl and
Peter Gedeck and
Donovan Chin and
Peter Hunt and
Mika K. Lindvall and
Katrin Spiegel and
Clayton Springer and
Scott Biller and
Christoph L. Buenemann and
Takanori Kanazawa and
Mitsunori Kato and
Richard A. Lewis and
Eric J. Martin and
Valery R. Polyakov and
Ruben Tommasi and
John H. Van Drie and
Brian Vash and
Lewis Whitehead and
Yongjin Xu and
Ruben Abagyan and
Eugene Raush and
Maxim Totrov},
title = {{FOCUS} - Development of a Global Communication and Modeling Platform
for Applied and Computational Medicinal Chemists},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {4},
pages = {896--908},
year = {2015},
url = {https://doi.org/10.1021/ci500598e},
doi = {10.1021/CI500598E},
timestamp = {Tue, 05 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/StieflGCHLSSBBK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HusbyBKAC15,
author = {Jarmila Husby and
Giovanni Bottegoni and
Irina Kufareva and
Ruben Abagyan and
Andrea Cavalli},
title = {Structure-Based Predictions of Activity Cliffs},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {5},
pages = {1062--1076},
year = {2015},
url = {https://doi.org/10.1021/ci500742b},
doi = {10.1021/CI500742B},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/HusbyBKAC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GeidlVBPIJAK15,
author = {Stanislav Geidl and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Veronika Bendov{\'{a}} and
Luk{\'{a}}s Petrusek and
Crina{-}Maria Ionescu and
Zdenek Jurka and
Ruben Abagyan and
Jaroslav Koca},
title = {How Does the Methodology of 3D Structure Preparation Influence the
Quality of p\emph{K}\({}_{\mbox{a}}\) Prediction?},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {6},
pages = {1088--1097},
year = {2015},
url = {https://doi.org/10.1021/ci500758w},
doi = {10.1021/CI500758W},
timestamp = {Thu, 23 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/GeidlVBPIJAK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GabrielsenKSWRKKANCSB14,
author = {Mari Gabrielsen and
Rafal Kurczab and
Agata Siwek and
Malgorzata Wolak and
Aina Westrheim Ravna and
Kurt Kristiansen and
Irina Kufareva and
Ruben Abagyan and
Gabriel Nowak and
Zdzislaw Chilmonczyk and
Ingebrigt Sylte and
Andrzej J. Bojarski},
title = {Identification of Novel Serotonin Transporter Compounds by Virtual
Screening},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {3},
pages = {933--943},
year = {2014},
url = {https://doi.org/10.1021/ci400742s},
doi = {10.1021/CI400742S},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/GabrielsenKSWRKKANCSB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/VarekovaGISBSAK13,
author = {Radka Svobodov{\'{a}} Varekov{\'{a}} and
Stanislav Geidl and
Crina{-}Maria Ionescu and
Ondrej Skrehota and
Tom{\'{a}}s Bouchal and
David Sehnal and
Ruben Abagyan and
Jaroslav Koca},
title = {Predicting pKa values from {EEM} atomic charges},
journal = {J. Cheminformatics},
volume = {5},
pages = {18},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-18},
doi = {10.1186/1758-2946-5-18},
timestamp = {Thu, 23 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/VarekovaGISBSAK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ChanSNLCWCMCLCAW13,
author = {Fung{-}Yi Chan and
Ning Sun and
Marco A. C. Neves and
Polo Chun{-}Hung Lam and
Wai{-}Hong Chung and
Lai{-}King Wong and
Ho{-}Yin Chow and
Dik{-}Lung Ma and
Pak{-}Ho Chan and
Yun{-}Chung Leung and
Tak{-}Hang Chan and
Ruben Abagyan and
Kwok{-}Yin Wong},
title = {Identification of a New Class of FtsZ Inhibitors by Structure-Based
Design and \emph{in Vitro} Screening},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {8},
pages = {2131--2140},
year = {2013},
url = {https://doi.org/10.1021/ci400203f},
doi = {10.1021/CI400203F},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ChanSNLCWCMCLCAW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Abagyan12,
author = {Ruben Abagyan},
title = {Computational chemistry in 25 years},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {1},
pages = {9--10},
year = {2012},
url = {https://doi.org/10.1007/s10822-011-9516-z},
doi = {10.1007/S10822-011-9516-Z},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Abagyan12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NevesTA12,
author = {Marco A. C. Neves and
Maxim Totrov and
Ruben Abagyan},
title = {Docking and scoring with {ICM:} the benchmarking results and strategies
for improvement},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {6},
pages = {675--686},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9547-0},
doi = {10.1007/S10822-012-9547-0},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/NevesTA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ChanNSTLCAW12,
author = {Fung{-}Yi Chan and
Marco A. C. Neves and
Ning Sun and
Man{-}Wah Tsang and
Yun{-}Chung Leung and
Tak{-}Hang Chan and
Ruben Abagyan and
Kwok{-}Yin Wong},
title = {Validation of the AmpC {\(\beta\)}-Lactamase Binding Site and Identification
of Inhibitors with Novel Scaffolds},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {5},
pages = {1367--1375},
year = {2012},
url = {https://doi.org/10.1021/ci300068m},
doi = {10.1021/CI300068M},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ChanNSTLCAW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RuedaTA12,
author = {Manuel Rueda and
Maxim Totrov and
Ruben Abagyan},
title = {ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather
than a Single Leader},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {10},
pages = {2705--2714},
year = {2012},
url = {https://doi.org/10.1021/ci3001088},
doi = {10.1021/CI3001088},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/RuedaTA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KufarevaIA12,
author = {Irina Kufareva and
Andrey V. Ilatovskiy and
Ruben Abagyan},
title = {Pocketome: an encyclopedia of small-molecule binding sites in 4D},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {535--540},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr825},
doi = {10.1093/NAR/GKR825},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KufarevaIA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BordnerZA11,
author = {Andrew J. Bordner and
Barry Zorman and
Ruben Abagyan},
title = {Efficient molecular mechanics simulations of the folding, orientation,
and assembly of peptides in lipid bilayers using an implicit atomic
solvation model},
journal = {J. Comput. Aided Mol. Des.},
volume = {25},
number = {10},
pages = {895--911},
year = {2011},
url = {https://doi.org/10.1007/s10822-011-9470-9},
doi = {10.1007/S10822-011-9470-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BordnerZA11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/VarekovaGISKSBAHK11,
author = {Radka Svobodov{\'{a}} Varekov{\'{a}} and
Stanislav Geidl and
Crina{-}Maria Ionescu and
Ondrej Skrehota and
Michal Kudera and
David Sehnal and
Tom{\'{a}}s Bouchal and
Ruben Abagyan and
Heinrich J. Huber and
Jaroslav Koca},
title = {Predicting p\emph{K}\({}_{\mbox{a}}\) Values of Substituted Phenols
from Atomic Charges: Comparison of Different Quantum Mechanical Methods
and Charge Distribution Schemes},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {8},
pages = {1795--1806},
year = {2011},
url = {https://doi.org/10.1021/ci200133w},
doi = {10.1021/CI200133W},
timestamp = {Thu, 23 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/VarekovaGISKSBAHK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuedaKRA10,
author = {Manuel Rueda and
Vsevolod Katritch and
Eugene Raush and
Ruben Abagyan},
title = {SimiCon: a web tool for protein-ligand model comparison through calculation
of equivalent atomic contacts},
journal = {Bioinform.},
volume = {26},
number = {21},
pages = {2784--2785},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq504},
doi = {10.1093/BIOINFORMATICS/BTQ504},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuedaKRA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/GrigoryanKTA10,
author = {A. V. Grigoryan and
Irina Kufareva and
Maxim Totrov and
Ruben Abagyan},
title = {Spatial chemical distance based on atomic property fields},
journal = {J. Comput. Aided Mol. Des.},
volume = {24},
number = {3},
pages = {173--182},
year = {2010},
url = {https://doi.org/10.1007/s10822-009-9316-x},
doi = {10.1007/S10822-009-9316-X},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/GrigoryanKTA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ParkKA10,
author = {So{-}Jung Park and
Irina Kufareva and
Ruben Abagyan},
title = {Improved docking, screening and selectivity prediction for small molecule
nuclear receptor modulators using conformational ensembles},
journal = {J. Comput. Aided Mol. Des.},
volume = {24},
number = {5},
pages = {459--471},
year = {2010},
url = {https://doi.org/10.1007/s10822-010-9362-4},
doi = {10.1007/S10822-010-9362-4},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ParkKA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RuedaBA10,
author = {Manuel Rueda and
Giovanni Bottegoni and
Ruben Abagyan},
title = {Recipes for the Selection of Experimental Protein Conformations for
Virtual Screening},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {1},
pages = {186--193},
year = {2010},
url = {https://doi.org/10.1021/ci9003943},
doi = {10.1021/CI9003943},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/RuedaBA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GarzonLPKAFC09,
author = {Jos{\'{e}} Ignacio Garz{\'{o}}n and
Jos{\'{e}} Ram{\'{o}}n L{\'{o}}pez{-}Blanco and
Carles Pons and
Julio A. Kovacs and
Ruben Abagyan and
Juan Fern{\'{a}}ndez{-}Recio and
Pablo Chac{\'{o}}n},
title = {{FRODOCK:} a new approach for fast rotational protein-protein docking},
journal = {Bioinform.},
volume = {25},
number = {19},
pages = {2544--2551},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp447},
doi = {10.1093/BIOINFORMATICS/BTP447},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GarzonLPKAFC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/ReynoldsKA09,
author = {Kimberly A. Reynolds and
Vsevolod Katritch and
Ruben Abagyan},
title = {Identifying conformational changes of the beta\({}_{\mbox{2}}\) adrenoceptor
that enable accurate prediction of ligand/receptor interactions and
screening for {GPCR} modulators},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {5},
pages = {273--288},
year = {2009},
url = {https://doi.org/10.1007/s10822-008-9257-9},
doi = {10.1007/S10822-008-9257-9},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/ReynoldsKA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RuedaBA09,
author = {Manuel Rueda and
Giovanni Bottegoni and
Ruben Abagyan},
title = {Consistent Improvement of Cross-Docking Results Using Binding Site
Ensembles Generated with Elastic Network Normal Modes},
journal = {J. Chem. Inf. Model.},
volume = {49},
number = {3},
pages = {716--725},
year = {2009},
url = {https://doi.org/10.1021/ci8003732},
doi = {10.1021/CI8003732},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/RuedaBA09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BottegoniKTA08,
author = {Giovanni Bottegoni and
Irina Kufareva and
Maxim Totrov and
Ruben Abagyan},
title = {A new method for ligand docking to flexible receptors by dual alanine
scanning and refinement {(SCARE)}},
journal = {J. Comput. Aided Mol. Des.},
volume = {22},
number = {5},
pages = {311--325},
year = {2008},
url = {https://doi.org/10.1007/s10822-008-9188-5},
doi = {10.1007/S10822-008-9188-5},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BottegoniKTA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NicolaSA08,
author = {George Nicola and
Colin A. Smith and
Ruben Abagyan},
title = {New Method for the Assessment of All Drug-Like Pockets Across a Structural
Genome},
journal = {J. Comput. Biol.},
volume = {15},
number = {3},
pages = {231--240},
year = {2008},
url = {https://doi.org/10.1089/cmb.2007.0178},
doi = {10.1089/CMB.2007.0178},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/NicolaSA08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LeeCKAFYY08,
author = {Hui Sun Lee and
Jiwon Choi and
Irina Kufareva and
Ruben Abagyan and
Anton V. Filikov and
Young Yang and
Sukjoon Yoon},
title = {Optimization of High Throughput Virtual Screening by Combining Shape-Matching
and Docking Methods},
journal = {J. Chem. Inf. Model.},
volume = {48},
number = {3},
pages = {489--497},
year = {2008},
url = {https://doi.org/10.1021/ci700376c},
doi = {10.1021/CI700376C},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LeeCKAFYY08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GarzonKAC07,
author = {Jos{\'{e}} Ignacio Garz{\'{o}}n and
Julio A. Kovacs and
Ruben Abagyan and
Pablo Chac{\'{o}}n},
title = {ADP{\_}EM: fast exhaustive multi-resolution docking for high-throughput
coverage},
journal = {Bioinform.},
volume = {23},
number = {4},
pages = {427--433},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl625},
doi = {10.1093/BIOINFORMATICS/BTL625},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GarzonKAC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GarzonKAC07a,
author = {Jos{\'{e}} Ignacio Garz{\'{o}}n and
Julio A. Kovacs and
Ruben Abagyan and
Pablo Chac{\'{o}}n},
title = {DFprot: a webtool for predicting local chain deformability},
journal = {Bioinform.},
volume = {23},
number = {7},
pages = {901--902},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm014},
doi = {10.1093/BIOINFORMATICS/BTM014},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GarzonKAC07a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/KatritchBTDRTAJH07,
author = {Vsevolod Katritch and
Chelsea M. Byrd and
Vladimir Tseitin and
Dongcheng Dai and
Eugene Raush and
Maxim Totrov and
Ruben Abagyan and
Robert Jordan and
Dennis E. Hruby},
title = {Discovery of small molecule inhibitors of ubiquitin-like poxvirus
proteinase {I7L} using homology modeling and covalent docking approaches},
journal = {J. Comput. Aided Mol. Des.},
volume = {21},
number = {10-11},
pages = {549--558},
year = {2007},
url = {https://doi.org/10.1007/s10822-007-9138-7},
doi = {10.1007/S10822-007-9138-7},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/KatritchBTDRTAJH07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BudagyanA06,
author = {Levon Budagyan and
Ruben Abagyan},
title = {Weighted quality estimates in machine learning},
journal = {Bioinform.},
volume = {22},
number = {21},
pages = {2597--2603},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl458},
doi = {10.1093/BIOINFORMATICS/BTL458},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BudagyanA06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BordnerA05,
author = {Andrew J. Bordner and
Ruben Abagyan},
title = {{REVCOM:} a robust Bayesian method for evolutionary rate estimation},
journal = {Bioinform.},
volume = {21},
number = {10},
pages = {2315--2321},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti347},
doi = {10.1093/BIOINFORMATICS/BTI347},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BordnerA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/TetkoAO05,
author = {Igor V. Tetko and
Ruben Abagyan and
Tudor I. Oprea},
title = {Surrogate data - a secure way to share corporate data},
journal = {J. Comput. Aided Mol. Des.},
volume = {19},
number = {9-10},
pages = {749--764},
year = {2005},
url = {https://doi.org/10.1007/s10822-005-9013-3},
doi = {10.1007/S10822-005-9013-3},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/TetkoAO05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarsdenA04,
author = {Brian Marsden and
Ruben Abagyan},
title = {{SAD} - a normalized structural alignment database: improving sequence-structure
alignments},
journal = {Bioinform.},
volume = {20},
number = {15},
pages = {2333--2344},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth244},
doi = {10.1093/BIOINFORMATICS/BTH244},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarsdenA04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BursulayaTAB03,
author = {Badry D. Bursulaya and
Maxim Totrov and
Ruben Abagyan and
Charles L. Brooks III},
title = {Comparative study of several algorithms for flexible ligand docking},
journal = {J. Comput. Aided Mol. Des.},
volume = {17},
number = {11},
pages = {755--763},
year = {2003},
url = {https://doi.org/10.1023/B:JCAM.0000017496.76572.6f},
doi = {10.1023/B:JCAM.0000017496.76572.6F},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/BursulayaTAB03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/KatritchTA03,
author = {Vsevolod Katritch and
Maxim Totrov and
Ruben Abagyan},
title = {{ICFF:} {A} new method to incorporate implicit flexibility into an
internal coordinate force field},
journal = {J. Comput. Chem.},
volume = {24},
number = {2},
pages = {254--265},
year = {2003},
url = {https://doi.org/10.1002/jcc.10091},
doi = {10.1002/JCC.10091},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/KatritchTA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhouA02,
author = {Yingyao Zhou and
Ruben Abagyan},
title = {Match-Only Integral Distribution {(MOID)} Algorithm for high-density
oligonucleotide array analysis},
journal = {{BMC} Bioinform.},
volume = {3},
pages = {3},
year = {2002},
url = {https://doi.org/10.1186/1471-2105-3-3},
doi = {10.1186/1471-2105-3-3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhouA02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/Fernandez-RecioTA02,
author = {Juan Fern{\'{a}}ndez{-}Recio and
Maxim Totrov and
Ruben Abagyan},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Screened Charge Electrostatic Model in Protein-Protein Docking Simulations},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {552--565},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/fernandez-recio.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/Fernandez-RecioTA02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Abagyan02,
author = {Ruben Abagyan},
editor = {Gene Myers and
Sridhar Hannenhalli and
David Sankoff and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Computational structural proteomics and virtual ligand screening},
booktitle = {Proceedings of the Sixth Annual International Conference on Computational
Biology, {RECOMB} 2002, Washington, DC, USA, April 18-21, 2002},
pages = {1},
publisher = {{ACM}},
year = {2002},
url = {https://doi.org/10.1145/565196.565197},
doi = {10.1145/565196.565197},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Abagyan02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/CardozoBA00,
author = {Timothy Cardozo and
Serge Batalov and
Ruben Abagyan},
title = {Estimating Local Backbone Structural Deviation in Homology Models},
journal = {Comput. Chem.},
volume = {24},
number = {1},
pages = {13--31},
year = {2000},
url = {https://doi.org/10.1016/S0097-8485(00)80004-2},
doi = {10.1016/S0097-8485(00)80004-2},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/CardozoBA00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/FilikovMVGCAJ00,
author = {Anton V. Filikov and
Venkatraman Mohan and
Timothy A. Vickers and
Richard H. Griffey and
P. Dan Cook and
Ruben Abagyan and
Thomas L. James},
title = {Identification of ligands for {RNA} targets via structure-based virtual
screening: {HIV-1} {TAR}},
journal = {J. Comput. Aided Mol. Des.},
volume = {14},
number = {6},
pages = {593--610},
year = {2000},
url = {https://doi.org/10.1023/A:1008121029716},
doi = {10.1023/A:1008121029716},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/FilikovMVGCAJ00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pnas/SchapiraRSA00,
author = {Matthieu Schapira and
Bruce M. Raaka and
Herbert H. Samuels and
Ruben Abagyan},
title = {Rational discovery of novel nuclear hormone receptor antagonists},
journal = {Proc. Natl. Acad. Sci. {USA}},
volume = {97},
number = {3},
pages = {1008--1013},
year = {2000},
url = {https://doi.org/10.1073/pnas.97.3.1008},
doi = {10.1073/PNAS.97.3.1008},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pnas/SchapiraRSA00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/TotrovA99,
author = {Maxim Totrov and
Ruben Abagyan},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Derivation of sensitive discrimination potential for virtual ligand
screening},
booktitle = {Proceedings of the Third Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1999, Lyon, France, April
11-14, 1999},
pages = {312--320},
publisher = {{ACM}},
year = {1999},
url = {https://doi.org/10.1145/299432.299509},
doi = {10.1145/299432.299509},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recomb/TotrovA99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Abagyan98,
author = {Ruben Abagyan},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Challenges of biomolecular structure prediction (abstract)},
booktitle = {Proceedings of the Second Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1998, New York, NY, USA,
March 22-25, 1998},
pages = {1},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/279069.279075},
doi = {10.1145/279069.279075},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Abagyan98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/AbagyanBCT97,
author = {Ruben Abagyan and
Serge Batalov and
Timothy Cardozo and
Maxim Totrov},
title = {From fold recognition to flexible docking},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1997,
Kloster Irsee, Bavaria, Germany, September 1997},
pages = {9--10},
publisher = {Oxford University Press},
year = {1997},
timestamp = {Fri, 02 Aug 2019 15:48:15 +0200},
biburl = {https://dblp.org/rec/conf/gcb/AbagyanBCT97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ArgosA94,
author = {Patrick Argos and
Ruben Abagyan},
title = {The Protein Folding Problem: Finding a Few Minimums in a Near Infinite
Space},
journal = {Comput. Chem.},
volume = {18},
number = {3},
pages = {225--231},
year = {1994},
url = {https://doi.org/10.1016/0097-8485(94)85017-8},
doi = {10.1016/0097-8485(94)85017-8},
timestamp = {Mon, 18 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/ArgosA94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/AbagyanTK94,
author = {Ruben Abagyan and
Maxim Totrov and
Dmitry Kuznetsov},
title = {{ICM} - {A} New Method for Protein Modeling and Design: Applications
to Docking and Strucutre Prediction from the Distorted Native Conformation},
journal = {J. Comput. Chem.},
volume = {15},
number = {5},
pages = {488--506},
year = {1994},
url = {https://doi.org/10.1002/jcc.540150503},
doi = {10.1002/JCC.540150503},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/AbagyanTK94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/TotrovA94,
author = {Maxim Totrov and
Ruben Abagyan},
title = {Efficient Parallelization of the Energy, Surface, and Dericative Calculations
for Internal Coordinate Mechanics},
journal = {J. Comput. Chem.},
volume = {15},
number = {10},
pages = {1105--1112},
year = {1994},
url = {https://doi.org/10.1002/jcc.540151006},
doi = {10.1002/JCC.540151006},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/TotrovA94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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