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2010 – today
- 2019
[j42]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. Journal of Computer-Aided Molecular Design 33(1): 35-46 (2019)- 2018
- [j41]Polo Chun-Hung Lam, Ruben Abagyan, Maxim Totrov:
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. Journal of Computer-Aided Molecular Design 32(1): 187-198 (2018) - 2017
- [j40]Dawid Warszycki, Manuel Rueda, Stefan Mordalski, Kurt Kristiansen, Grzegorz Satala, Krzysztof Rataj, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Ruben Abagyan, Andrzej J. Bojarski:
From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. Journal of Chemical Information and Modeling 57(2): 311-321 (2017) - 2015
- [j39]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: 59:1-59:10 (2015) - [j38]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 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. Journal of Chemical Information and Modeling 55(4): 896-908 (2015) - [j37]Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli:
Structure-Based Predictions of Activity Cliffs. Journal of Chemical Information and Modeling 55(5): 1062-1076 (2015) - [j36]Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca:
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? Journal of Chemical Information and Modeling 55(6): 1088-1097 (2015) - 2014
- [j35]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. Journal of Chemical Information and Modeling 54(3): 933-943 (2014) - 2013
- [j34]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: 18 (2013) - [j33]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:
Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening. Journal of Chemical Information and Modeling 53(8): 2131-2140 (2013) - 2012
- [j32]Ruben Abagyan:
Computational chemistry in 25 years. Journal of Computer-Aided Molecular Design 26(1): 9-10 (2012) - [j31]Marco A. C. Neves, Maxim Totrov, Ruben Abagyan:
Docking and scoring with ICM: the benchmarking results and strategies for improvement. Journal of Computer-Aided Molecular Design 26(6): 675-686 (2012) - [j30]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. Journal of Chemical Information and Modeling 52(5): 1367-1375 (2012) - [j29]Manuel Rueda, Maxim Totrov, Ruben Abagyan:
ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. Journal of Chemical Information and Modeling 52(10): 2705-2714 (2012) - [j28]Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Research 40(Database-Issue): 535-540 (2012) - 2011
- [j27]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. Journal of Computer-Aided Molecular Design 25(10): 895-911 (2011) - [j26]Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca:
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. Journal of Chemical Information and Modeling 51(8): 1795-1806 (2011) - 2010
- [j25]Manuel Rueda, Vsevolod Katritch, Eugene Raush, Ruben Abagyan:
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts. Bioinformatics 26(21): 2784-2785 (2010) - [j24]A. V. Grigoryan, Irina Kufareva, Maxim Totrov, Ruben Abagyan:
Spatial chemical distance based on atomic property fields. Journal of Computer-Aided Molecular Design 24(3): 173-182 (2010) - [j23]So-Jung Park, Irina Kufareva, Ruben Abagyan:
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. Journal of Computer-Aided Molecular Design 24(5): 459-471 (2010) - [j22]Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. Journal of Chemical Information and Modeling 50(1): 186-193 (2010)
2000 – 2009
- 2009
- [j21]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. Bioinformatics 25(19): 2544-2551 (2009) - [j20]Kimberly A. Reynolds, Vsevolod Katritch, Ruben Abagyan:
Identifying conformational changes of the beta2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators. Journal of Computer-Aided Molecular Design 23(5): 273-288 (2009) - [j19]Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. Journal of Chemical Information and Modeling 49(3): 716-725 (2009) - 2008
- [j18]Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan:
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). Journal of Computer-Aided Molecular Design 22(5): 311-325 (2008) - [j17]George Nicola, Colin A. Smith, Ruben Abagyan:
New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome. Journal of Computational Biology 15(3): 231-240 (2008) - [j16]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. Journal of Chemical Information and Modeling 48(3): 489-497 (2008) - 2007
- [j15]José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics 23(4): 427-433 (2007) - [j14]José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
DFprot: a webtool for predicting local chain deformability. Bioinformatics 23(7): 901-902 (2007) - [j13]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. Journal of Computer-Aided Molecular Design 21(10-11): 549-558 (2007) - 2006
- [j12]Levon Budagyan, Ruben Abagyan:
Weighted quality estimates in machine learning. Bioinformatics 22(21): 2597-2603 (2006) - 2005
- [j11]Andrew J. Bordner, Ruben Abagyan:
REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinformatics 21(10): 2315-2321 (2005) - [j10]Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea:
Surrogate data - a secure way to share corporate data. Journal of Computer-Aided Molecular Design 19(9-10): 749-764 (2005) - 2004
- [j9]Brian Marsden, Ruben Abagyan:
SAD - a normalized structural alignment database: improving sequence-structure alignments. Bioinformatics 20(15): 2333-2344 (2004) - 2003
- [j8]Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III:
Comparative study of several algorithms for flexible ligand docking. Journal of Computer-Aided Molecular Design 17(11): 755-763 (2003) - [j7]Vsevolod Katritch, Maxim Totrov, Ruben Abagyan:
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. Journal of Computational Chemistry 24(2): 254-265 (2003) - 2002
- [j6]Yingyao Zhou, Ruben Abagyan:
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. BMC Bioinformatics 3: 3 (2002) - [c5]Juan Fernández-Recio, Maxim Totrov, Ruben Abagyan:
Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. Pacific Symposium on Biocomputing 2002: 552-565 - [c4]
- 2000
- [j5]Timothy Cardozo, Serge Batalov, Ruben Abagyan:
Estimating Local Backbone Structural Deviation in Homology Models. Computers & Chemistry 24(1): 13-31 (2000) - [j4]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. Journal of Computer-Aided Molecular Design 14(6): 593-610 (2000)
1990 – 1999
- 1999
- [c3]Maxim Totrov, Ruben Abagyan:
Derivation of sensitive discrimination potential for virtual ligand screening. RECOMB 1999: 312-320 - 1998
- [c2]
- 1997
- [c1]Ruben Abagyan, Serge Batalov, Timothy Cardozo, Maxim Totrov:
From fold recognition to flexible docking. German Conference on Bioinformatics 1997: 9-10 - 1994
- [j3]Patrick Argos, Ruben Abagyan:
The Protein Folding Problem: Finding a Few Minimums in a Near Infinite Space. Computers & Chemistry 18(3): 225-231 (1994) - [j2]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. Journal of Computational Chemistry 15(5): 488-506 (1994) - [j1]Maxim Totrov, Ruben Abagyan:
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. Journal of Computational Chemistry 15(10): 1105-1112 (1994)
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