Ruben Abagyan

Orcid: 0000-0001-9309-2976

According to our database1, Ruben Abagyan authored at least 54 papers between 1994 and 2022.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 




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

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

Druggable exosites of the human kino-pocketome.
J. Comput. Aided Mol. Des., 2020

Extended Multitarget Pharmacology of Anticancer Drugs.
J. Chem. Inf. Model., 2019

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.
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

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.
J. Comput. Aided Mol. Des., 2018

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT<sub>1A</sub> Receptor Case Study.
J. Chem. Inf. Model., 2017

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

Structure-Based Predictions of Activity Cliffs.
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

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

Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and <i>in Vitro</i> Screening.
J. Chem. Inf. Model., 2013

Predicting pKa values from EEM atomic charges.
J. Cheminformatics, 2013

Pocketome: an encyclopedia of small-molecule binding sites in 4D.
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

Computational chemistry in 25 years.
J. Comput. Aided Mol. Des., 2012

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

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

Spatial chemical distance based on atomic property fields.
J. Comput. Aided Mol. Des., 2010

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.
Bioinform., 2010

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

FRODOCK: a new approach for fast rotational protein-protein docking.
Bioinform., 2009

Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods.
J. Chem. Inf. Model., 2008

New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome.
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

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.
J. Comput. Aided Mol. Des., 2007

DFprot: a webtool for predicting local chain deformability.
Bioinform., 2007

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.
Bioinform., 2007

Weighted quality estimates in machine learning.
Bioinform., 2006

Surrogate data - a secure way to share corporate data.
J. Comput. Aided Mol. Des., 2005

REVCOM: a robust Bayesian method for evolutionary rate estimation.
Bioinform., 2005

SAD - a normalized structural alignment database: improving sequence-structure alignments.
Bioinform., 2004

ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field.
J. Comput. Chem., 2003

Comparative study of several algorithms for flexible ligand docking.
J. Comput. Aided Mol. Des., 2003

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

Computational structural proteomics and virtual ligand screening.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Screened Charge Electrostatic Model in Protein-Protein Docking Simulations.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Rational discovery of novel nuclear hormone receptor antagonists.
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

Estimating Local Backbone Structural Deviation in Homology Models.
Comput. Chem., 2000

Derivation of sensitive discrimination potential for virtual ligand screening.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Challenges of biomolecular structure prediction (abstract).
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

From fold recognition to flexible docking.
Proceedings of the German Conference on Bioinformatics, 1997

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

The Protein Folding Problem: Finding a Few Minimums in a Near Infinite Space.
Comput. Chem., 1994