List of works - Ruben Abagyan

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site

scientific article published on 18 February 2019

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action

scientific article published on 13 February 2019

3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis

scholarly article

A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway

scientific article

A natural product-like inhibitor of NEDD8-activating enzyme

scientific article published on 14 January 2011

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

scientific article published on 14 February 2008

A new method for publishing three-dimensional content

scientific article

A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer

scientific article

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader ⬇️

scientific article published on September 17, 2012

Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling

scientific article published on 9 April 2015

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges

scientific article published on 24 July 2014

Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada

scientific article

Algorithms for high-density oligonucleotide array

scientific article

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

scientific article published on 2 April 2015

An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network

scientific article published on 20 July 2016

An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels

scientific article

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens

scientific article published on 19 September 2017

Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes

scientific article

Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A.

scientific article

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry

scientific article

Comparative study of several algorithms for flexible ligand docking

scientific article published in November 2003

Compound activity prediction using models of binding pockets or ligand properties in 3D.

scientific article

Comprehensive identification of "druggable" protein ligand binding sites.

scientific article

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

scientific article

Conserved Binding Mode of Human β 2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

scientific article

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

scientific article published on March 2009

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

scientific article published on 14 September 2021

Damped-dynamics flexible fitting

scientific article

De novo discovery of serotonin N-acetyltransferase inhibitors

scientific article

Defining the CD59-C9 binding interaction

scientific article

Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells

scientific article published on 26 September 2018

Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant

scientific article published on 02 October 2019

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking

scientific article

Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening

scientific article published on 26 April 2007

Discovery of novel membrane binding structures and functions

scientific article

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

scientific article

Disseminating structural genomics data to the public: from a data dump to an animated story

scientific article

Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin

scientific article

Docking and scoring with ICM: the benchmarking results and strategies for improvement ⬇️

scientific article published on May 9, 2012

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping

scientific article published on January 2014

Druggability of SCF ubiquitin ligase-protein interfaces

scientific article published in January 2005

Druggable exosites of the human kino-pocketome

scientific article published on 10 January 2020

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model ⬇️

scientific article published on September 9, 2011

Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling

scientific article

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs

scientific article

Extended Multitarget Pharmacology of Anticancer Drugs

scientific article published on 03 May 2019

FRODOCK: a new approach for fast rotational protein-protein docking

scientific article published on 20 July 2009

Flexible ligand docking to multiple receptor conformations: a practical alternative

scientific article

Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor

scientific article published on 10 June 2017

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

scientific article published in January 2009

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study

scientific article published on 05 January 2017

Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor

scientific article published on 8 May 2009

GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex

scientific article

GPCR agonist binding revealed by modeling and crystallography

scientific article published on 6 September 2011

High-quality and universal empirical atomic charges for chemoinformatics applications

scientific article (publication date: 2015)

Histidine(7.36(305)) in the conserved peptide receptor activation domain of the gonadotropin releasing hormone receptor couples peptide binding and receptor activation

scientific article

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

scientific article published on 11 June 2015

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

scientific article (publication date: May 1994)

Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Naegleria fowleri Sterol Δ8-Δ7-Isomerase and Phenotypic Assays

scientific article published on 17 October 2019

Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening

scientific article

Identification of novel serotonin transporter compounds by virtual screening

scientific article published on 26 February 2014

Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

scientific article

Identifying ligands at orphan GPCRs: current status using structure-based approaches

scientific article published on 2 February 2016

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

scientific article

In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species

scientific article

In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α.

scientific article

Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux

scientific article published on 17 February 2017

Lanosterol reverses protein aggregation in cataracts

scientific journal article

Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds

scientific article

Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping

scientific article

Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics

scientific article published on 25 February 2022

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis

scientific article

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

scientific article

Methods of protein structure comparison

scientific article

Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands

scientific article published on September 2009

Molecular Basis for Binding and Subtype Selectivity of 1,4-Benzodiazepine Antagonist Ligands of the Cholecystokinin Receptor ⬇️

scientific article published on March 30, 2012

Molecular Basis of Secretin Docking to Its Intact Receptor Using Multiple Photolabile Probes Distributed throughout the Pharmacophore ⬇️

scientific article published on May 12, 2011

Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol

scientific article

Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases

scientific article

Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents

scientific article

Molecular modeling and mutagenesis of gap junction channels

scientific article published on 23 March 2007

New method for the assessment of all drug-like pockets across a structural genome

scientific article published on April 2008

Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma

scientific article published on 20 September 2019

Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies

scientific article published on 20 March 2012

Nuclear hormone receptor targeted virtual screening

scientific article

Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening

scientific article

Optimization of high throughput virtual screening by combining shape-matching and docking methods

scientific article

Orphan receptor ligand discovery by pickpocketing pharmacological neighbors

scientific article published on 19 December 2016

P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma

scientific article

PIER: protein interface recognition for structural proteomics.

scientific article

PeptiSite: a structural database of peptide binding sites in 4D.

scientific article

Phenotypic, chemical and functional characterization of cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential anthelmintic drug target

scientific article published on 13 July 2017

Pocketome via comprehensive identification and classification of ligand binding envelopes.

scientific article

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

scientific article published on November 12, 2011

Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications

scientific article

Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain.

scientific article published on 18 April 2018

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes

scientific article published in August 2011

Predicting pKa values from EEM atomic charges

scientific article published on 10 April 2013

Protein-RNA and Protein-Protein Recognition by Dual KH1/2 Domains of the Neuronal Splicing Factor Nova-1

scientific article

Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics

scientific article

Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity

scientific article (publication date: 2014)

Recipes for the selection of experimental protein conformations for virtual screening

scientific article

Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling

scientific article

Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction

scientific article published on 24 March 2007

SGC--structural biology and human health: a new approach to publishing structural biology results

scientific article

Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment

scientific article

Sequence-conserved and antibody-accessible sites in the V1V2 domain of HIV-1 gp120 envelope protein

scientific article

Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors

scientific article

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

scientific article

Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease

scientific article

Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization

scientific article

Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins

scientific article published in December 2005

Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates

scientific article

Soft protein–protein docking in internal coordinates ⬇️

scientific article published on February 1, 2002

Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding

scientific article published on 08 May 2008

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

scientific article published on August 2011

Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation

scientific article

Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine

scientific article

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

scientific article

Structure based prediction of subtype-selectivity for adenosine receptor antagonists

scientific article

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

scientific article published on June 2017

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

scientific article published on 07 December 2016

Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation

scientific article published on 24 February 2009

Structure of the human histamine H1 receptor complex with doxepin

scientific article

Structure-based discovery of natural-product-like TNF-α inhibitors

scientific article published on 16 March 2010

Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists

scientific article

Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors

scientific article

Structure-based predictions of activity cliffs

scientific article published on 11 May 2015

Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists

scientific article

Surrogate data--a secure way to share corporate data

scientific article

Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors

scientific article published on 11 April 2013

Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors

scientific article

Systematic exploitation of multiple receptor conformations for virtual ligand screening

scientific article

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function

scientific article published on 14 December 2012

The flexible pocketome engine for structural chemogenomics

scientific article

The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure

scientific article

The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening

scientific article

The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers

scientific article

The transthyretin-related protein family

scientific article published in February 2003

Three-dimensional Structure of the EphB2 Receptor in Complex with an Antagonistic Peptide Reveals a Novel Mode of Inhibition

scientific article

Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states

scientific article published on December 2008

Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration

scientific article published on September 2011

Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks ⬇️

scientific article published on April 19, 2012

Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention

scientific article

Validation of the AmpC β-lactamase binding site and identification of inhibitors with novel scaffolds

scientific article published on May 4, 2012

Viral infection controlled by a calcium-dependent lipid-binding module in ALIX.

scientific article

Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor

scientific article

X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action

scientific article published on 11 February 2016

List of works by Ruben Abagyan

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action

3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis

A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway

A natural product-like inhibitor of NEDD8-activating enzyme

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

A new method for publishing three-dimensional content

A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader ⬇️

Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges

Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada

Algorithms for high-density oligonucleotide array

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

An Organic Anion Transporter 1 (OAT1)-centered Metabolic Network

An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens

Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes

Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A.

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry

Comparative study of several algorithms for flexible ligand docking

Compound activity prediction using models of binding pockets or ligand properties in 3D.

Comprehensive identification of "druggable" protein ligand binding sites.

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

Conserved Binding Mode of Human β 2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

Damped-dynamics flexible fitting

De novo discovery of serotonin N-acetyltransferase inhibitors

Defining the CD59-C9 binding interaction

Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells

Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking

Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening

Discovery of novel membrane binding structures and functions

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

Disseminating structural genomics data to the public: from a data dump to an animated story

Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin

Docking and scoring with ICM: the benchmarking results and strategies for improvement ⬇️

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping

Druggability of SCF ubiquitin ligase-protein interfaces

Druggable exosites of the human kino-pocketome

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model ⬇️

Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs

Extended Multitarget Pharmacology of Anticancer Drugs

FRODOCK: a new approach for fast rotational protein-protein docking

Flexible ligand docking to multiple receptor conformations: a practical alternative

Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study

Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor

GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex

GPCR agonist binding revealed by modeling and crystallography

High-quality and universal empirical atomic charges for chemoinformatics applications

Histidine(7.36(305)) in the conserved peptide receptor activation domain of the gonadotropin releasing hormone receptor couples peptide binding and receptor activation

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Naegleria fowleri Sterol Δ8-Δ7-Isomerase and Phenotypic Assays

Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening

Identification of novel serotonin transporter compounds by virtual screening

Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

Identifying ligands at orphan GPCRs: current status using structure-based approaches

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species

In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α.

Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux

Lanosterol reverses protein aggregation in cataracts

Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds

Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping

Mapping the gene network landscape of Alzheimer's disease through integrating genomics and transcriptomics

Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

Methods of protein structure comparison

Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands

Molecular Basis for Binding and Subtype Selectivity of 1,4-Benzodiazepine Antagonist Ligands of the Cholecystokinin Receptor ⬇️

Molecular Basis of Secretin Docking to Its Intact Receptor Using Multiple Photolabile Probes Distributed throughout the Pharmacophore ⬇️

Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol

Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases