Ruben Abagyan

Publication Activity (10 Years)

Years Active: 1994-2022
Publications (10 Years): 9

Top Topics

Grand Challenge

Chemical Compounds

Virtual Screening

Cervical Cancer

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Cheminformatics

PLoS Comput. Biol.

Publications

Sara Brin Rosenthal, Hao Wang, Da Shi, Cin Liu, Ruben Abagyan, Linda K. McEvoy, Chi-Hua Chen
Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics. PLoS Comput. Biol. 18 (2) (2022)
Eugene Raush, Ruben Abagyan, Maxim Totrov
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. J. Chem. Inf. Model. 62 (23) (2022)
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, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross Cagan
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput. Biol. 17 (9) (2021)
George Nicola, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
Druggable exosites of the human kino-pocketome. J. Comput. Aided Mol. Des. 34 (3) (2020)
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. J. Comput. Aided Mol. Des. 33 (1) (2019)
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 33 (12) (2019)
Da Shi, Feroz Khan, Ruben Abagyan
Extended Multitarget Pharmacology of Anticancer Drugs. J. Chem. Inf. Model. 59 (6) (2019)
Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. J. Comput. Aided Mol. Des. 32 (1) (2018)
Dawid Warszycki, Manuel Rueda, Stefan Mordalski, Kurt Kristiansen, Grzegorz Satala, Krzysztof Rataj, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Ruben Abagyan, Andrzej J. Bojarski
Receptor Case Study. J. Chem. Inf. Model. 57 (2) (2017)
Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca
Prediction? J. Chem. Inf. Model. 55 (6) (2015)
Stanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca
High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics 7 (2015)
Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli
Structure-Based Predictions of Activity Cliffs. J. Chem. Inf. Model. 55 (5) (2015)
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 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
FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. J. Chem. Inf. Model. 55 (4) (2015)
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
Identification of Novel Serotonin Transporter Compounds by Virtual Screening. J. Chem. Inf. Model. 54 (3) (2014)
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca
Predicting pKa values from EEM atomic charges. J. Cheminformatics 5 (2013)
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
Screening. J. Chem. Inf. Model. 53 (8) (2013)
Manuel Rueda, Maxim Totrov, Ruben Abagyan
ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. J. Chem. Inf. Model. 52 (10) (2012)
Ruben Abagyan
Computational chemistry in 25 years. J. Comput. Aided Mol. Des. 26 (1) (2012)
Fung-Yi Chan, Marco A. C. Neves, Ning Sun, Man-Wah Tsang, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong
Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds. J. Chem. Inf. Model. 52 (5) (2012)
Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 40 (Database-Issue) (2012)
Marco A. C. Neves, Maxim Totrov, Ruben Abagyan
Docking and scoring with ICM: the benchmarking results and strategies for improvement. J. Comput. Aided Mol. Des. 26 (6) (2012)
Andrew J. Bordner, Barry Zorman, Ruben Abagyan
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. 25 (10) (2011)
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51 (8) (2011)
Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. J. Chem. Inf. Model. 50 (1) (2010)
Manuel Rueda, Vsevolod Katritch, Eugene Raush, Ruben Abagyan
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinform. 26 (21) (2010)
So-Jung Park, Irina Kufareva, Ruben Abagyan
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J. Comput. Aided Mol. Des. 24 (5) (2010)
A. V. Grigoryan, Irina Kufareva, Maxim Totrov, Ruben Abagyan
Spatial chemical distance based on atomic property fields. J. Comput. Aided Mol. Des. 24 (3) (2010)
Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan
adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. J. Comput. Aided Mol. Des. 23 (5) (2009)
Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. J. Chem. Inf. Model. 49 (3) (2009)
José Ignacio Garzón, José Ramón López-Blanco, Carles Pons, Julio A. Kovacs, Ruben Abagyan, Juan Fernández-Recio, Pablo Chacón
FRODOCK: a new approach for fast rotational protein-protein docking. Bioinform. 25 (19) (2009)
Hui Sun Lee, Jiwon Choi, Irina Kufareva, Ruben Abagyan, Anton V. Filikov, Young Yang, Sukjoon Yoon
Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods. J. Chem. Inf. Model. 48 (3) (2008)
George Nicola, Colin A. Smith, Ruben Abagyan
New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome. J. Comput. Biol. 15 (3) (2008)
Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J. Comput. Aided Mol. Des. 22 (5) (2008)
José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón
DFprot: a webtool for predicting local chain deformability. Bioinform. 23 (7) (2007)
Vsevolod Katritch, Chelsea M. Byrd, Vladimir Tseitin, Dongcheng Dai, Eugene Raush, Maxim Totrov, Ruben Abagyan, Robert Jordan, Dennis E. Hruby
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J. Comput. Aided Mol. Des. 21 (10-11) (2007)
José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinform. 23 (4) (2007)
Levon Budagyan, Ruben Abagyan
Weighted quality estimates in machine learning. Bioinform. 22 (21) (2006)
Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea
Surrogate data - a secure way to share corporate data. J. Comput. Aided Mol. Des. 19 (9-10) (2005)
Andrew J. Bordner, Ruben Abagyan
REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinform. 21 (10) (2005)
Brian Marsden, Ruben Abagyan
SAD - a normalized structural alignment database: improving sequence-structure alignments. Bioinform. 20 (15) (2004)
Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III
Comparative study of several algorithms for flexible ligand docking. J. Comput. Aided Mol. Des. 17 (11) (2003)
Vsevolod Katritch, Maxim Totrov, Ruben Abagyan
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. J. Comput. Chem. 24 (2) (2003)
Ruben Abagyan
Computational structural proteomics and virtual ligand screening. RECOMB (2002)
Yingyao Zhou, Ruben Abagyan
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. BMC Bioinform. 3 (2002)
Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan
Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. Pacific Symposium on Biocomputing (2002)
Anton V. Filikov, Venkatraman Mohan, Timothy A. Vickers, Richard H. Griffey, P. Dan Cook, Ruben Abagyan, Thomas L. James
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J. Comput. Aided Mol. Des. 14 (6) (2000)
Matthieu Schapira, Bruce M. Raaka, Herbert H. Samuels, Ruben Abagyan
Rational discovery of novel nuclear hormone receptor antagonists. Proc. Natl. Acad. Sci. USA 97 (3) (2000)
Timothy Cardozo, Serge Batalov, Ruben Abagyan
Estimating Local Backbone Structural Deviation in Homology Models. Comput. Chem. 24 (1) (2000)
Maxim Totrov, Ruben Abagyan
Derivation of sensitive discrimination potential for virtual ligand screening. RECOMB (1999)
Ruben Abagyan
Challenges of biomolecular structure prediction (abstract). RECOMB (1998)
Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov
From fold recognition to flexible docking. German Conference on Bioinformatics (1997)
Patrick Argos, Ruben Abagyan
The Protein Folding Problem: Finding a Few Minimums in a Near Infinite Space. Comput. Chem. 18 (3) (1994)
Maxim Totrov, Ruben Abagyan
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. J. Comput. Chem. 15 (10) (1994)
Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov
ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation. J. Comput. Chem. 15 (5) (1994)