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2020 – today
- 2022
[j49]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): 5896-5906 (2022)- [j48]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) - 2021
- [j47]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 L. 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) - 2020
- [j46]George Nicola, Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Druggable exosites of the human kino-pocketome. J. Comput. Aided Mol. Des. 34(3): 219-230 (2020)
2010 – 2019
- 2019
- [j45]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): 35-46 (2019) - [j44]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): 1057-1069 (2019) - [j43]Da Shi, Feroz Khan, Ruben Abagyan:
Extended Multitarget Pharmacology of Anticancer Drugs. J. Chem. Inf. Model. 59(6): 3006-3017 (2019) - 2018
- [j42]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): 187-198 (2018) - 2017
- [j41]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. J. Chem. Inf. Model. 57(2): 311-321 (2017) - 2015
- [j40]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) - [j39]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:
FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. J. Chem. Inf. Model. 55(4): 896-908 (2015) - [j38]Jarmila Husby, Giovanni Bottegoni, Irina Kufareva, Ruben Abagyan, Andrea Cavalli:
Structure-Based Predictions of Activity Cliffs. J. Chem. Inf. Model. 55(5): 1062-1076 (2015) - [j37]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? J. Chem. Inf. Model. 55(6): 1088-1097 (2015) - 2014
- [j36]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): 933-943 (2014) - 2013
- [j35]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) - [j34]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. J. Chem. Inf. Model. 53(8): 2131-2140 (2013) - 2012
- [j33]Ruben Abagyan:
Computational chemistry in 25 years. J. Comput. Aided Mol. Des. 26(1): 9-10 (2012) - [j32]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): 675-686 (2012) - [j31]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): 1367-1375 (2012) - [j30]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): 2705-2714 (2012) - [j29]Irina Kufareva, Andrey V. Ilatovskiy, Ruben Abagyan:
Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 40(Database-Issue): 535-540 (2012) - 2011
- [j28]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): 895-911 (2011) - [j27]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. J. Chem. Inf. Model. 51(8): 1795-1806 (2011) - 2010
- [j26]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): 2784-2785 (2010) - [j25]A. V. Grigoryan, Irina Kufareva, Maxim Totrov, Ruben Abagyan:
Spatial chemical distance based on atomic property fields. J. Comput. Aided Mol. Des. 24(3): 173-182 (2010) - [j24]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): 459-471 (2010) - [j23]Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. J. Chem. Inf. Model. 50(1): 186-193 (2010)
2000 – 2009
- 2009
- [j22]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): 2544-2551 (2009) - [j21]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. J. Comput. Aided Mol. Des. 23(5): 273-288 (2009) - [j20]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): 716-725 (2009) - 2008
- [j19]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): 311-325 (2008) - [j18]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): 231-240 (2008) - [j17]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): 489-497 (2008) - 2007
- [j16]José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinform. 23(4): 427-433 (2007) - [j15]José Ignacio Garzón, Julio A. Kovacs, Ruben Abagyan, Pablo Chacón:
DFprot: a webtool for predicting local chain deformability. Bioinform. 23(7): 901-902 (2007) - [j14]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): 549-558 (2007) - 2006
- [j13]Levon Budagyan, Ruben Abagyan:
Weighted quality estimates in machine learning. Bioinform. 22(21): 2597-2603 (2006) - 2005
- [j12]Andrew J. Bordner, Ruben Abagyan:
REVCOM: a robust Bayesian method for evolutionary rate estimation. Bioinform. 21(10): 2315-2321 (2005) - [j11]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): 749-764 (2005) - 2004
- [j10]Brian Marsden, Ruben Abagyan:
SAD - a normalized structural alignment database: improving sequence-structure alignments. Bioinform. 20(15): 2333-2344 (2004) - 2003
- [j9]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): 755-763 (2003) - [j8]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): 254-265 (2003) - 2002
- [j7]Yingyao Zhou, Ruben Abagyan:
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis. BMC Bioinform. 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]Ruben Abagyan:
Computational structural proteomics and virtual ligand screening. RECOMB 2002: 1 - 2000
- [j6]Timothy Cardozo, Serge Batalov, Ruben Abagyan:
Estimating Local Backbone Structural Deviation in Homology Models. Comput. Chem. 24(1): 13-31 (2000) - [j5]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): 593-610 (2000) - [j4]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): 1008-1013 (2000)
1990 – 1999
- 1999
- [c3]Maxim Totrov, Ruben Abagyan:
Derivation of sensitive discrimination potential for virtual ligand screening. RECOMB 1999: 312-320 - 1998
- [c2]Ruben Abagyan:
Challenges of biomolecular structure prediction (abstract). RECOMB 1998: 1 - 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. Comput. Chem. 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. J. Comput. Chem. 15(5): 488-506 (1994) - [j1]Maxim Totrov, Ruben Abagyan:
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. J. Comput. Chem. 15(10): 1105-1112 (1994)
Coauthor Index
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