Ruben Abagyan

54 papers B 3Misc 1Journal 49Unranked 1
YearRankTypeTitle / Venue / Authors
2022 J jnl
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules.
J. Chem. Inf. Model.
Eugene Raush, Ruben Abagyan, Maxim Totrov
2022 J jnl
Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics.
PLoS Comput. Biol.
Sara Brin Rosenthal, Hao Wang, Da Shi, Cin Liu, Ruben Abagyan, Linda K. McEvoy, Chi-Hua Chen
2021 J jnl
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.
PLoS Comput. Biol.
Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alexander Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
2020 J jnl
Druggable exosites of the human kino-pocketome.
J. Comput. Aided Mol. Des.
George Nicola, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
2019 J jnl
Extended Multitarget Pharmacology of Anticancer Drugs.
J. Chem. Inf. Model.
Da Shi, Feroz Khan, Ruben Abagyan
2019 J jnl
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.
J. Comput. Aided Mol. Des.
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
2019 J jnl
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.
J. Comput. Aided Mol. Des.
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
2018 J jnl
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
J. Comput. Aided Mol. Des.
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
2017 J jnl
From Homology Models to a Set of Predictive Binding Pockets-a 5-HT
J. Chem. Inf. Model.
Dawid Warszycki, Manuel Rueda, Stefan Mordalski, Kurt Kristiansen, Grzegorz Satala, Krzysztof Rataj, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Ruben Abagyan, Andrzej J. Bojarski
2015 J jnl
FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists.
J. Chem. Inf. Model.
Nikolaus Stiefl, Peter Gedeck, Donovan Chin, Peter Hunt, Mika K. Lindvall, Katrin Spiegel, Clayton Springer, Scott Biller, Christoph L. Buenemann, Takanori Kanazawa, Mitsunori Kato, Richard A. Lewis, Eric J. Martin, Valery R. Polyakov, Ruben Tommasi, John H. Van Drie, Brian Vash, Lewis Whitehead, Yongjin Xu, Ruben Abagyan, Eugene Raush, Maxim Totrov
2015 J jnl
High-quality and universal empirical atomic charges for chemoinformatics applications.
J. Cheminformatics
Stanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca
2015 J jnl
How Does the Methodology of 3D Structure Preparation Influence the Quality of p
J. Chem. Inf. Model.
Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca
2015 J jnl
Structure-Based Predictions of Activity Cliffs.
J. Chem. Inf. Model.
Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli
2014 J jnl
Identification of Novel Serotonin Transporter Compounds by Virtual Screening.
J. Chem. Inf. Model.
Mari Gabrielsen, Rafal Kurczab, Agata Siwek, Malgorzata Wolak, Aina Westrheim Ravna, Kurt Kristiansen, Irina Kufareva, Ruben Abagyan, Gabriel Nowak, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Andrzej J. Bojarski
2013 J jnl
Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and
J. Chem. Inf. Model.
Fung-Yi Chan, Ning Sun, Marco A. C. Neves, Polo Chun-Hung Lam, Wai-Hong Chung, Lai-King Wong, Ho-Yin Chow, Dik-Lung Ma, Pak-Ho Chan, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong
2013 J jnl
Predicting pKa values from EEM atomic charges.
J. Cheminformatics
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca
2012 J jnl
ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader.
J. Chem. Inf. Model.
Manuel Rueda, Maxim Totrov, Ruben Abagyan
2012 J jnl
Computational chemistry in 25 years.
J. Comput. Aided Mol. Des.
Ruben Abagyan
2012 J jnl
Docking and scoring with ICM: the benchmarking results and strategies for improvement.
J. Comput. Aided Mol. Des.
Marco A. C. Neves, Maxim Totrov, Ruben Abagyan
2012 J jnl
Pocketome: an encyclopedia of small-molecule binding sites in 4D.
Nucleic Acids Res.
Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
2012 J jnl
Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds.
J. Chem. Inf. Model.
Fung-Yi Chan, Marco A. C. Neves, Ning Sun, Man-Wah Tsang, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong
2011 J jnl
Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model.
J. Comput. Aided Mol. Des.
Andrew J. Bordner, Barry Zorman, Ruben Abagyan
2011 J jnl
Predicting p
J. Chem. Inf. Model.
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
2010 J jnl
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles.
J. Comput. Aided Mol. Des.
So-Jung Park, Irina Kufareva, Ruben Abagyan
2010 J jnl
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening.
J. Chem. Inf. Model.
Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan
2010 J jnl
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
Bioinform.
Manuel Rueda, Vsevolod Katritch, Eugene Raush, Ruben Abagyan
2010 J jnl
Spatial chemical distance based on atomic property fields.
J. Comput. Aided Mol. Des.
A. V. Grigoryan, Irina Kufareva, Maxim Totrov, Ruben Abagyan
2009 J jnl
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes.
J. Chem. Inf. Model.
Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan
2009 J jnl
FRODOCK: a new approach for fast rotational protein-protein docking.
Bioinform.
José Ignacio Garzón, José Ramón López-Blanco, Carles Pons, Julio A. Kovacs, Ruben Abagyan, Juan Fernández-Recio, Pablo Chacón
2009 J jnl
Identifying conformational changes of the beta
J. Comput. Aided Mol. Des.
Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan
2008 J jnl
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).
J. Comput. Aided Mol. Des.
Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan
2008 J jnl
New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome.
J. Comput. Biol.
George Nicola, Colin A. Smith, Ruben Abagyan
2008 J jnl
Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods.
J. Chem. Inf. Model.
Hui Sun Lee, Jiwon Choi, Irina Kufareva, Ruben Abagyan, Anton V. Filikov, Young Yang, Sukjoon Yoon
2007 J jnl
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.
Bioinform.
José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón
2007 J jnl
DFprot: a webtool for predicting local chain deformability.
Bioinform.
José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón
2007 J jnl
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.
J. Comput. Aided Mol. Des.
Vsevolod Katritch, Chelsea M. Byrd, Vladimir Tseitin, Dongcheng Dai, Eugene Raush, Maxim Totrov, Ruben Abagyan, Robert Jordan, Dennis E. Hruby
2006 J jnl
Weighted quality estimates in machine learning.
Bioinform.
Levon Budagyan, Ruben Abagyan
2005 J jnl
REVCOM: a robust Bayesian method for evolutionary rate estimation.
Bioinform.
Andrew J. Bordner, Ruben Abagyan
2005 J jnl
Surrogate data - a secure way to share corporate data.
J. Comput. Aided Mol. Des.
Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea
2004 J jnl
SAD - a normalized structural alignment database: improving sequence-structure alignments.
Bioinform.
Brian Marsden, Ruben Abagyan
2003 J jnl
Comparative study of several algorithms for flexible ligand docking.
J. Comput. Aided Mol. Des.
Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III
2003 J jnl
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field.
J. Comput. Chem.
Vsevolod Katritch, Maxim Totrov, Ruben Abagyan
2002 B conf
Computational structural proteomics and virtual ligand screening.
RECOMB
Ruben Abagyan
2002 J jnl
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis.
BMC Bioinform.
Yingyao Zhou, Ruben Abagyan
2002 Misc conf
Screened Charge Electrostatic Model in Protein-Protein Docking Simulations.
Pacific Symposium on Biocomputing
Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan
2000 J jnl
Estimating Local Backbone Structural Deviation in Homology Models.
Comput. Chem.
Timothy Cardozo, Serge Batalov, Ruben Abagyan
2000 J jnl
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.
J. Comput. Aided Mol. Des.
Anton V. Filikov, Venkatraman Mohan, Timothy A. Vickers, Richard H. Griffey, P. Dan Cook, Ruben Abagyan, Thomas L. James
2000 J jnl
Rational discovery of novel nuclear hormone receptor antagonists.
Proc. Natl. Acad. Sci. USA
Matthieu Schapira, Bruce M. Raaka, Herbert H. Samuels, Ruben Abagyan
1999 B conf
Derivation of sensitive discrimination potential for virtual ligand screening.
RECOMB
Maxim Totrov, Ruben Abagyan
1998 B conf
Challenges of biomolecular structure prediction (abstract).
RECOMB
Ruben Abagyan
1997 — conf
From fold recognition to flexible docking.
German Conference on Bioinformatics
Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov
1994 J jnl
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics.
J. Comput. Chem.
Maxim Totrov, Ruben Abagyan
1994 J jnl
ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation.
J. Comput. Chem.
Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov
1994 J jnl
The Protein Folding Problem: Finding a Few Minimums in a Near Infinite Space.
Comput. Chem.
Patrick Argos, Ruben Abagyan