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Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies.
Alshahrani M, Parikh V, Foley B, Raisinghani N, Verkhivker G. Alshahrani M, et al. Among authors: raisinghani n. bioRxiv [Preprint]. 2024 Dec 20:2024.12.19.629520. doi: 10.1101/2024.12.19.629520. bioRxiv. 2024. PMID: 39763975 Free PMC article. Preprint.
Assessing Structures and Conformational Ensembles of Apo and Holo Protein States Using Randomized Alanine Sequence Scanning Combined with Shallow Subsampling in AlphaFold2 : Insights and Lessons from Predictions of Functional Allosteric Conformations.
Raisinghani N, Parikh V, Foley B, Verkhivker G. Raisinghani N, et al. bioRxiv [Preprint]. 2024 Nov 6:2024.11.04.621947. doi: 10.1101/2024.11.04.621947. bioRxiv. 2024. PMID: 39574675 Free PMC article. Preprint.
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.
Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. J Phys Chem B. 2024 Nov 14;128(45):11088-11107. doi: 10.1021/acs.jpcb.4c04985. Epub 2024 Nov 1. J Phys Chem B. 2024. PMID: 39485490
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.
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Raisinghani N, et al. Viruses. 2024 Sep 13;16(9):1458. doi: 10.3390/v16091458. Viruses. 2024. PMID: 39339934 Free PMC article.
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.
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Raisinghani N, et al. bioRxiv [Preprint]. 2024 Jul 10:2024.07.09.602810. doi: 10.1101/2024.07.09.602810. bioRxiv. 2024. Update in: Viruses. 2024 Sep 13;16(9):1458. doi: 10.3390/v16091458 PMID: 39026832 Free PMC article. Updated. Preprint.
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.
Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker GM. Raisinghani N, et al. J Chem Theory Comput. 2024 Jun 25;20(12):5317-5336. doi: 10.1021/acs.jctc.4c00222. Epub 2024 Jun 12. J Chem Theory Comput. 2024. PMID: 38865109
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.
Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. bioRxiv [Preprint]. 2024 May 18:2024.05.17.594786. doi: 10.1101/2024.05.17.594786. bioRxiv. 2024. PMID: 38798650 Free PMC article. Preprint.
23 results