The Protein Folding Problem: Finding a Few Minimums in a Near Infinite Space. - Patrick Argos; Ruben Abagyan (Comput. Chem., 1994)

ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation. - Ruben Abagyan; Maxim Totrov; Dmitry Kuznetsov (J. Comput. Chem., 1994)

Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. - Maxim Totrov; Ruben Abagyan (J. Comput. Chem., 1994)

From fold recognition to flexible docking. - Ruben Abagyan; Serge Batalov; Timothy Cardozo; Maxim Totrov (German Conference on Bioinformatics, 1997)

Challenges of biomolecular structure prediction (abstract). - Ruben Abagyan (RECOMB, 1998)

Derivation of sensitive discrimination potential for virtual ligand screening. - Maxim Totrov; Ruben Abagyan (RECOMB, 1999)

Estimating Local Backbone Structural Deviation in Homology Models. - Timothy Cardozo; Serge Batalov; Ruben Abagyan (Comput. Chem., 2000)

Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. - Anton V. Filikov; Venkatraman Mohan; Timothy A. Vickers; Richard H. Griffey; P. Dan Cook; Ruben Abagyan; Thomas L. James (J. Comput. Aided Mol. Des., 2000)

Rational discovery of novel nuclear hormone receptor antagonists. - Matthieu Schapira; Bruce M. Raaka; Herbert H. Samuels; Ruben Abagyan (Proc. Natl. Acad. Sci. USA, 2000)

Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. - Juan Fernández-Recio; Maxim Totrov; Ruben Abagyan (Pacific Symposium on Biocomputing, 2002)

Computational structural proteomics and virtual ligand screening. - Ruben Abagyan (RECOMB, 2002)

Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. - Yingyao Zhou; Ruben Abagyan (BMC Bioinform., 2002)

Comparative study of several algorithms for flexible ligand docking. - Badry D. Bursulaya; Maxim Totrov; Ruben Abagyan; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2003)

ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. - Vsevolod Katritch; Maxim Totrov; Ruben Abagyan (J. Comput. Chem., 2003)

SAD - a normalized structural alignment database: improving sequence-structure alignments. - Brian Marsden; Ruben Abagyan (Bioinform., 2004)

REVCOM: a robust Bayesian method for evolutionary rate estimation. - Andrew J. Bordner; Ruben Abagyan (Bioinform., 2005)

Surrogate data - a secure way to share corporate data. - Igor V. Tetko; Ruben Abagyan; Tudor I. Oprea (J. Comput. Aided Mol. Des., 2005)

Weighted quality estimates in machine learning. - Levon Budagyan; Ruben Abagyan (Bioinform., 2006)

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. - José Ignacio Garzón; Julio A. Kovacs; Ruben Abagyan; Pablo Chacón (Bioinform., 2007)

DFprot: a webtool for predicting local chain deformability. - José Ignacio Garzón; Julio A. Kovacs; Ruben Abagyan; Pablo Chacón (Bioinform., 2007)

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. - Vsevolod Katritch; Chelsea M. Byrd; Vladimir Tseitin; Dongcheng Dai; Eugene Raush; Maxim Totrov; Ruben Abagyan; Robert Jordan; Dennis E. Hruby (J. Comput. Aided Mol. Des., 2007)

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). - Giovanni Bottegoni; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2008)

New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome. - George Nicola; Colin A. Smith; Ruben Abagyan (J. Comput. Biol., 2008)

Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods. - Hui Sun Lee; Jiwon Choi; Irina Kufareva; Ruben Abagyan; Anton V. Filikov; Young Yang; Sukjoon Yoon (J. Chem. Inf. Model., 2008)

FRODOCK: a new approach for fast rotational protein-protein docking. - José Ignacio Garzón; José Ramón López-Blanco; Carles Pons; Julio A. Kovacs; Ruben Abagyan; Juan Fernández-Recio; Pablo Chacón (Bioinform., 2009)

Identifying conformational changes of the beta2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. - Kimberly A. Reynolds; Vsevolod Katritch; Ruben Abagyan (J. Comput. Aided Mol. Des., 2009)

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2009)

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. - Manuel Rueda; Vsevolod Katritch; Eugene Raush; Ruben Abagyan (Bioinform., 2010)

Spatial chemical distance based on atomic property fields. - A. V. Grigoryan; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2010)

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. - So-Jung Park; Irina Kufareva; Ruben Abagyan (J. Comput. Aided Mol. Des., 2010)

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. - Manuel Rueda; Giovanni Bottegoni; Ruben Abagyan (J. Chem. Inf. Model., 2010)

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. - Andrew J. Bordner; Barry Zorman; Ruben Abagyan (J. Comput. Aided Mol. Des., 2011)

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Michal Kudera; David Sehnal; Tomás Bouchal; Ruben Abagyan; Heinrich J. Huber; Jaroslav Koca (J. Chem. Inf. Model., 2011)

Computational chemistry in 25 years. - Ruben Abagyan (J. Comput. Aided Mol. Des., 2012)

Docking and scoring with ICM: the benchmarking results and strategies for improvement. - Marco A. C. Neves; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2012)

Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds. - Fung-Yi Chan; Marco A. C. Neves; Ning Sun; Man-Wah Tsang; Yun-Chung Leung; Tak-Hang Chan; Ruben Abagyan; Kwok-Yin Wong (J. Chem. Inf. Model., 2012)

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. - Manuel Rueda; Maxim Totrov; Ruben Abagyan (J. Chem. Inf. Model., 2012)

Pocketome: an encyclopedia of small-molecule binding sites in 4D. - Irina Kufareva; Andrey V. Ilatovskiy; Ruben Abagyan (Nucleic Acids Res., 2012)

Predicting pKa values from EEM atomic charges. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Tomás Bouchal; David Sehnal; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2013)

Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening. - 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; et al. (J. Chem. Inf. Model., 2013)

Identification of Novel Serotonin Transporter Compounds by Virtual Screening. - 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 (J. Chem. Inf. Model., 2014)

High-quality and universal empirical atomic charges for chemoinformatics applications. - Stanislav Geidl; Tomás Bouchal; Tomás Racek; Radka Svobodová Vareková; Václav Hejret; Ales Krenek; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2015)

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? - Stanislav Geidl; Radka Svobodová Vareková; Veronika Bendová; Lukás Petrusek; Crina-Maria Ionescu; Zdenek Jurka; Ruben Abagyan; Jaroslav Koca (J. Chem. Inf. Model., 2015)

Structure-Based Predictions of Activity Cliffs. - Jarmila Husby; Giovanni Bottegoni; Irina Kufareva; Ruben Abagyan; Andrea Cavalli (J. Chem. Inf. Model., 2015)

FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. - 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; et al. (J. Chem. Inf. Model., 2015)

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. - Dawid Warszycki; Manuel Rueda; Stefan Mordalski; Kurt Kristiansen; Grzegorz Satala; Krzysztof Rataj; Zdzislaw Chilmonczyk; Ingebrigt Sylte; Ruben Abagyan; Andrzej J. Bojarski (J. Chem. Inf. Model., 2017)

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2018)

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2019)

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2019)

Extended Multitarget Pharmacology of Anticancer Drugs. - Da Shi; Feroz Khan; Ruben Abagyan (J. Chem. Inf. Model., 2019)

Druggable exosites of the human kino-pocketome. - George Nicola; Irina Kufareva; Andrey V. Ilatovskiy; Ruben Abagyan (J. Comput. Aided Mol. Des., 2020)

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. - 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; et al. (PLoS Comput. Biol., 2021)

Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. - Eugene Raush; Ruben Abagyan; Maxim Totrov (J. Chem. Inf. Model., 2022)

Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. - Sara Brin Rosenthal; Hao Wang 128; Da Shi; Cin Liu; Ruben Abagyan; Linda K. McEvoy; Chi-Hua Chen (PLoS Comput. Biol., 2022)