Author

Grace Gupta

Chapman University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Assay:protein structure· 3 Approach:mechanistic / dynamical model· 2 Research Focus:protein structure prediction· 2 Organism:virus· 2 Research Focus:protein folding & dynamics· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Gennady M. VerkhivkeriD· 3 shared Mohammed AlshahraniiD· 3 shared Nishank RaisinghaniiD· 3 shared Peng TaoiD· 2 shared Sian XiaoiD· 2 shared Hao TianiD· 1 shared

Activity by Year

2024-2024 · peak 3/yr

Co-Author Collaboration Network

6 top collaborators · 15 mutual co-author links

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3 shared papersBiophysics

Gennady M. VerkhivkerORCID

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3 papers

Recent·Most cited

Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape

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

Viruses · Sep 13, 2024Peer-reviewedBiophysics

Prediction of Conformational Ensembles and Structural Effects of State-Switching Allosteric Mutants in the Protein Kinases Using Comparative Analysis of AlphaFold2 Adaptations with Sequence Masking and Shallow Subsampling

Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M. Verkhivker

This study adapts AlphaFold2 to predict conformational ensembles of allosteric ABL kinase mutants, showing that sequence masking and subsampling improve prediction of structural state shifts caused by mutations.

bioRxiv · May 17, 2024 · PreprintBiophysics

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

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

This study uses AlphaFold2 and molecular dynamics to predict conformational ensembles and binding mechanisms of SARS-CoV-2 Omicron variants, showing agreement with experimental data.

bioRxiv · Apr 2, 2024 · PreprintBiophysics