Search filters

Authors whose works are in public domain in at least one jurisdiction

List of works by Gennady Verkhivker

A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding

scientific article

A systematic protocol for the characterization of Hsp90 modulators.

scientific article

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

scientific article published on 19 February 2019

Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling

scientific article

Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric Communications

scientific article published on 02 May 2019

Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains

scientific article published on 21 December 2017

Atomistic simulations of the HIV-1 protease folding inhibition

scientific article published on 28 March 2008

Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication

scientific article published on 16 October 2018

Cancer driver mutations in protein kinase genes

scientific article

Characterization of multiple stable conformers of the EC5 domain of E-cadherin and the interaction of EC5 with E-cadherin peptides.

scientific article published on June 2009

Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2

scientific article published on 04 November 2020

Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding

scientific article published on 12 June 2020

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

scientific article published on 26 April 2021

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective

scientific article

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

scientific article

Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations

scientific article published in May 2004

Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.

scientific article published in November 2003

Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases

scientific article

Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.

scientific article

Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs

scientific article published on 15 October 2008

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

scientific article published on 30 November 2015

Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks

scientific article published on 19 July 2019

Deciphering common failures in molecular docking of ligand-protein complexes.

scientific article

Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors.

scientific article published on 22 November 2016

Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study.

scientific article

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

scientific article published on 26 July 2021

Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones.

scientific article published on 2 May 2018

Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation

scientific article published on 23 March 2022

Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches

scientific article published on 15 January 2021

Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots

scientific article published on 17 June 2021

Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks

scientific article published on 21 January 2020

Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90.

scientific article published on 30 August 2010

Dynamics-based community analysis and perturbation response scanning of allosteric interaction networks in the TRAP1 chaperone structures dissect molecular linkage between conformational asymmetry and sequential ATP hydrolysis

scientific article published on 20 April 2018

Elucidation of the Hsp90 C-terminal inhibitor binding site

scientific article (publication date: 19 August 2011)

Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations ⬇️

scientific article published on January 1, 1996

Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

scientific article published in July 1995

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

scientific article published on 06 May 2003

Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone

scientific article published on 2 November 2017

Experimentally guided structural modeling and dynamics analysis of Hsp90-p53 interactions: allosteric regulation of the Hsp90 chaperone by a client protein.

scientific article

Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

scientific article

Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics.

scientific article published on 30 May 2007

Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90-Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation

scientific article published on 12 February 2018

Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations

scientific article

Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.

scientific article published in December 2001

Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides

scientific article published in January 2002

In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures.

scientific article published in March 2007

Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies

scientific article published on 30 April 2021

Integrated Computational Approaches and Tools forAllosteric Drug Discovery

scientific article published on 28 January 2020

Integrating ligand-based and protein-centric virtual screening of kinase inhibitors using ensembles of multiple protein kinase genes and conformations.

scientific article

Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations.

scientific article published on 11 June 2019

Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant

scientific article published on 09 June 2021

Leveraging Structural Diversity and Allosteric Regulatory Mechanisms of Protein Kinases in the Discovery of Small Molecule Inhibitors

scientific article

Locally enhanced sampling in free energy calculations: Application of mean field approximation to accurate calculation of free energy differences

Machine Learning Classification and Structure-Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes

article

Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity ⬇️

scientific article published on July 1, 1997

Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer

scientific article

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

scientific article

Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality.

scientific article published on 12 August 2015

Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins

scientific article published on 02 October 2020

Molecular anchors with large stability gaps ensure linear binding free energy relationships for hydrophobic substituents ⬇️

scientific article published on January 1, 1998

Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation.

scientific article

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

scientific article

Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface

scientific article published in August 2002

Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms

scientific article published on 19 September 2017

Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks

scientific article published on 22 July 2016

Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics

scientific article

Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-

scientific article published in February 2005

Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: hierarchy of structural loss from all-atom Monte Carlo simulations of p27Kip1 unfolding-unbinding and structural determinants of the binding mec

scientific article published on 01 December 2004

Quantifying intrinsic specificity: a potential complement to affinity in drug screening

scientific article published on 06 November 2007

Sequence and structure signatures of cancer mutation hotspots in protein kinases

scientific article

Sequence recognition of alpha-LFA-1-derived peptides by ICAM-1 cell receptors: inhibitors of T-cell adhesion.

scientific article published on September 2007

Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics ⬇️

scientific article published on July 16, 2012

Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects.

scientific article

Structural and computational biology of the molecular chaperone Hsp90: from understanding molecular mechanisms to computer-based inhibitor design.

scientific article published on January 2009

Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin ⬇️

scientific article published on July 1, 1997

Structural modifications of ICAM-1 cyclic peptides to improve the activity to inhibit heterotypic adhesion of T cells

scientific article published on 11 June 2008

Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.

scientific article

Structure-functional prediction and analysis of cancer mutation effects in protein kinases.

scientific article

The energy landscape analysis of cancer mutations in protein kinases

scientific article

The role of covalent dimerization on the physical and chemical stability of the EC1 domain of human E-cadherin.

scientific article published on October 2009

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions

scientific article

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

scientific article published on August 1996

Paulina is supported by:

About Paulina

Help