Ruben Abagyan
Orcid: 0000-0001-9309-2976
According to our database1,
Ruben Abagyan
authored at least 54 papers
between 1994 and 2022.
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Bibliography
2022
Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics.
PLoS Comput. Biol., 2022
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules.
J. Chem. Inf. Model., 2022
2021
Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.
PLoS Comput. Biol., 2021
2020
2019
J. Comput. Aided Mol. Des., 2019
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.
J. Comput. Aided Mol. Des., 2019
2018
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
J. Comput. Aided Mol. Des., 2018
2017
From Homology Models to a Set of Predictive Binding Pockets-a 5-HT<sub>1A</sub> Receptor Case Study.
J. Chem. Inf. Model., 2017
2015
FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists.
J. Chem. Inf. Model., 2015
How Does the Methodology of 3D Structure Preparation Influence the Quality of p<i>K</i><sub>a</sub> Prediction?
J. Chem. Inf. Model., 2015
High-quality and universal empirical atomic charges for chemoinformatics applications.
J. Cheminformatics, 2015
2014
J. Chem. Inf. Model., 2014
2013
Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and <i>in Vitro</i> Screening.
J. Chem. Inf. Model., 2013
2012
Nucleic Acids Res., 2012
ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader.
J. Chem. Inf. Model., 2012
Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds.
J. Chem. Inf. Model., 2012
Docking and scoring with ICM: the benchmarking results and strategies for improvement.
J. Comput. Aided Mol. Des., 2012
2011
Predicting p<i>K</i><sub>a</sub> Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes.
J. Chem. Inf. Model., 2011
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., 2011
2010
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening.
J. Chem. Inf. Model., 2010
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles.
J. Comput. Aided Mol. Des., 2010
J. Comput. Aided Mol. Des., 2010
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
Bioinform., 2010
2009
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes.
J. Chem. Inf. Model., 2009
Identifying conformational changes of the beta<sub>2</sub> adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators.
J. Comput. Aided Mol. Des., 2009
Bioinform., 2009
2008
Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods.
J. Chem. Inf. Model., 2008
J. Comput. Biol., 2008
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).
J. Comput. Aided Mol. Des., 2008
2007
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.
J. Comput. Aided Mol. Des., 2007
Bioinform., 2007
2006
2005
J. Comput. Aided Mol. Des., 2005
2004
SAD - a normalized structural alignment database: improving sequence-structure alignments.
Bioinform., 2004
2003
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field.
J. Comput. Chem., 2003
J. Comput. Aided Mol. Des., 2003
2002
Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis.
BMC Bioinform., 2002
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
2000
Proc. Natl. Acad. Sci. USA, 2000
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.
J. Comput. Aided Mol. Des., 2000
Comput. Chem., 2000
1999
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999
1998
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998
1997
From fold recognition to flexible docking.
Proceedings of the German Conference on Bioinformatics, 1997
1994
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics.
J. Comput. Chem., 1994
ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation.
J. Comput. Chem., 1994
Comput. Chem., 1994