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For: Ansari N, Rizzi V, Carloni P, Parrinello M. Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution. J Am Chem Soc 2021;143:12930-12934. [PMID: 34398611 PMCID: PMC8386029 DOI: 10.1021/jacs.1c05301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Evans D, Sheraz S, Lau AY. SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling. Proteins 2025. [PMID: 40026279 DOI: 10.1002/prot.26814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 01/22/2025] [Accepted: 02/18/2025] [Indexed: 03/05/2025]
2
Bemelmans MP, Cournia Z, Damm-Ganamet KL, Gervasio FL, Pande V. Computational advances in discovering cryptic pockets for drug discovery. Curr Opin Struct Biol 2025;90:102975. [PMID: 39778412 DOI: 10.1016/j.sbi.2024.102975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 11/27/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025]
3
Lee E, Rauscher S. The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery. Biochemistry 2025;64:32-46. [PMID: 39513739 DOI: 10.1021/acs.biochem.4c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
4
Zhang Y, Wang Y, Zhao Y, Hu R, Yuan H. Design of aggregation-induced emission materials for biosensing of molecules and cells. Biosens Bioelectron 2025;267:116805. [PMID: 39321612 DOI: 10.1016/j.bios.2024.116805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/17/2024] [Accepted: 09/19/2024] [Indexed: 09/27/2024]
5
Karrenbrock M, Borsatto A, Rizzi V, Lukauskis D, Aureli S, Luigi Gervasio F. Absolute Binding Free Energies with OneOPES. J Phys Chem Lett 2024;15:9871-9880. [PMID: 39302888 PMCID: PMC11457222 DOI: 10.1021/acs.jpclett.4c02352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/13/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
6
Evans D, Sheraz S, Lau A. SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595309. [PMID: 38826232 PMCID: PMC11142162 DOI: 10.1101/2024.05.22.595309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
7
Karrenbrock M, Rizzi V, Procacci P, Gervasio FL. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. J Phys Chem B 2024;128:1595-1605. [PMID: 38323915 DOI: 10.1021/acs.jpcb.3c06516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
8
Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024;64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
9
Rizzi V, Aureli S, Ansari N, Gervasio FL. OneOPES, a Combined Enhanced Sampling Method to Rule Them All. J Chem Theory Comput 2023;19:5731-5742. [PMID: 37603295 PMCID: PMC10500989 DOI: 10.1021/acs.jctc.3c00254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Indexed: 08/22/2023]
10
Ansari N, Rizzi V, Parrinello M. Water regulates the residence time of Benzamidine in Trypsin. Nat Commun 2022;13:5438. [PMID: 36114175 PMCID: PMC9481606 DOI: 10.1038/s41467-022-33104-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/01/2022] [Indexed: 12/11/2022]  Open
11
Cheng Y, Clark AE, Zhou J, He T, Li Y, Borum RM, Creyer MN, Xu M, Jin Z, Zhou J, Yim W, Wu Z, Fajtová P, O’Donoghue AJ, Carlin AF, Jokerst JV. Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells. ACS NANO 2022;16:12305-12317. [PMID: 35878004 PMCID: PMC9344892 DOI: 10.1021/acsnano.2c03219] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 05/06/2023]
12
Invernizzi M, Parrinello M. Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling. J Chem Theory Comput 2022;18:3988-3996. [PMID: 35617155 PMCID: PMC9202311 DOI: 10.1021/acs.jctc.2c00152] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
13
Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations. Chem Phys Lett 2022;794:139489. [PMID: 35221345 PMCID: PMC8863314 DOI: 10.1016/j.cplett.2022.139489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 12/16/2022]
14
Raucci U, Rizzi V, Parrinello M. Discover, Sample, and Refine: Exploring Chemistry with Enhanced Sampling Techniques. J Phys Chem Lett 2022;13:1424-1430. [PMID: 35119863 DOI: 10.1021/acs.jpclett.1c03993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
15
Parrinello M. Breviarium de Motu Simulato Ad Atomos Pertinenti. Isr J Chem 2022. [DOI: 10.1002/ijch.202100105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
16
Aminah NS, Abdjan MI, Wardana AP, Kristanti AN, Siswanto I, Rakhman KA, Takaya Y. The dolabellane diterpenes as potential inhibitors of the SARS-CoV-2 main protease: molecular insight of the inhibitory mechanism through computational studies. RSC Adv 2021;11:39455-39466. [PMID: 35492446 PMCID: PMC9044469 DOI: 10.1039/d1ra07584e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022]  Open
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