Grace Gupta

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

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Indexed papers

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datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 20 papers. Top paper: “Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms”.

Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00778

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43 citations

Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships

Physical Chemistry Chemical Physics(2023)10.1039/d3cp02042h

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16 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

From 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 Approaches

International Journal of Molecular Sciences(2023)10.3390/ijms24097747

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15 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites

Viruses(2023)10.3390/v15102073

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9 citations

Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557205

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Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.03.539337

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Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.20.541592

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Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.18.567697

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Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.11.571185

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Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance

Viruses(2024)10.3390/v16091458

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28 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00222

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17 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c01341

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17 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape

International Journal of Molecular Sciences(2024)10.3390/ijms25084281

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16 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations

Physical Chemistry Chemical Physics(2024)10.1039/d4cp01372g

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13 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking

International Journal of Molecular Sciences(2024)10.3390/ijms25094955

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6 citations

Gennady M. Verkhivker, Grace Gupta

AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c01857

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7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning

International Journal of Molecular Sciences(2024)10.3390/ijms251810082

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6 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04985

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5 citations

Mohammed Merae Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.02.587850

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7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.15.580591

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5 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more