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445(top 2%)
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citing journals

Top Articles

#TitleJournalYearCitations
1Integrated Computational Approaches and Tools for Allosteric Drug DiscoveryInternational Journal of Molecular Sciences202073
2Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike ProteinsJournal of Proteome Research202072
3Dynamic 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 SwitchesJournal of Physical Chemistry B202166
4Comparative 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 MutationsBiochemistry202162
5Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with AntibodiesJournal of Physical Chemistry B202160
6Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric CommunicationsJournal of Chemical Theory and Computation201946
7Dynamic 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 HotspotsJournal of Chemical Theory and Computation202139
8Dynamic 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 NetworksJournal of Chemical Information and Modeling202027
9Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and SignalingJournal of Chemical Information and Modeling202126
10Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron MutationsInternational Journal of Molecular Sciences202216
11Exploring Mechanisms of Communication Switching in the Hsp90-Cdc37 Regulatory Complexes with Client Kinases through Allosteric Coupling of Phosphorylation Sites: Perturbation-Based Modeling and Hierarchical Community Analysis of Residue Interaction NetworksJournal of Chemical Theory and Computation202015
12Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric PocketsInternational Journal of Molecular Sciences202215
13Making the invisible visible: Toward structural characterization of allosteric states, interaction networks, and allosteric regulatory mechanisms in protein kinasesCurrent Opinion in Structural Biology202113
14Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulationJournal of Biomolecular Structure and Dynamics202211
15Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape MechanismsACS Omega202111
16Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational ApproachesJournal of Chemical Information and Modeling202311
17Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction NetworksJournal of Chemical Information and Modeling202010
18Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G VariantACS Omega202110
19Biophysical Insight into the SARS-CoV2 Spike–ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational ApproachACS Omega20229
20Frustration-driven allosteric regulation and signal transmission in the SARS-CoV-2 spike omicron trimer structures: a crosstalk of the omicron mutation sites allosterically regulates tradeoffs of protein stability and conformational adaptabilityPhysical Chemistry Chemical Physics09
21Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody EngineeringInternational Journal of Molecular Sciences20228
22From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on “Allosteric Intersection” of Biochemical and Big Data ApproachesInternational Journal of Molecular Sciences20236
23Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron VariantInternational Journal of Molecular Sciences20225
24Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike VariantsJournal of Chemical Information and Modeling20225
25Acidulant effect on greening, reducing capacity, and tryptophan fluorescence of sunflower butter cookie dough during refrigerated storageJournal of the Science of Food and Agriculture20194
26Interpretable Machine Learning Models for Molecular Design of Tyrosine Kinase Inhibitors Using Variational Autoencoders and Perturbation-Based Approach of Chemical Space ExplorationInternational Journal of Molecular Sciences20224
27Arginine Methylation of the PGC-1α C-Terminus Is Temperature-DependentBiochemistry20234
28Dissecting Molecular Principles of the Hsp90 Chaperone Regulation by Allosteric Modulators Using a Hierarchical Simulation Approach and Network Modeling of Allosteric Interactions: Conformational Selection Dictates the Diversity of Protein Responses and Ligand-Specific Functional MechanismsJournal of Chemical Theory and Computation20203
29Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein StabilityInternational Journal of Molecular Sciences20222
30Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and AllosteryJournal of Physical Chemistry B20222
31Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentialsJournal of Chemical Physics20222
32Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 VariantsInternational Journal of Molecular Sciences20232
33Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape MechanismsBiomolecules20220