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For: Colizzi F, Orozco M. Probing allosteric regulations with coevolution-driven molecular simulations. Sci Adv 2021;7:eabj0786. [PMID: 34516882 PMCID: PMC8442858 DOI: 10.1126/sciadv.abj0786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Number Cited by Other Article(s)
1
Fenton AW, Hoffpauir ZA, Martin TA, Harris RA, Lamb AL. Are Allosteric Mechanisms Conserved Among Homologues? J Mol Biol 2025:169176. [PMID: 40306405 DOI: 10.1016/j.jmb.2025.169176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 04/10/2025] [Accepted: 04/24/2025] [Indexed: 05/02/2025]
2
Bonollo G, Trèves G, Komarov D, Mansoor S, Moroni E, Colombo G. Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity. J Phys Chem Lett 2025;16:3606-3615. [PMID: 40179097 PMCID: PMC12010417 DOI: 10.1021/acs.jpclett.5c00652] [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: 03/03/2025] [Revised: 03/28/2025] [Accepted: 04/01/2025] [Indexed: 04/05/2025]
3
Paloncýová M, Valério M, Dos Santos RN, Kührová P, Šrejber M, Čechová P, Dobchev DA, Balsubramani A, Banáš P, Agarwal V, Souza PCT, Otyepka M. Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery. Mol Pharm 2025;22:1110-1141. [PMID: 39879096 PMCID: PMC11881150 DOI: 10.1021/acs.molpharmaceut.4c00744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 01/06/2025] [Accepted: 01/06/2025] [Indexed: 01/31/2025]
4
Cui Q. Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses. J Mol Biol 2025:168998. [PMID: 39952349 DOI: 10.1016/j.jmb.2025.168998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 01/19/2025] [Accepted: 02/08/2025] [Indexed: 02/17/2025]
5
Zhang C, Zhang R, Qi Y, Wen X, Sun J, Xiao P. Exploring the Binding Mechanism of ADGRG2 Through Metadynamics and Biochemical Analysis. Int J Mol Sci 2024;26:167. [PMID: 39796025 PMCID: PMC11719512 DOI: 10.3390/ijms26010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 12/26/2024] [Accepted: 12/26/2024] [Indexed: 01/13/2025]  Open
6
Luo J, Song C, Cui W, Wang Q, Zhou Z, Han L. Precise redesign for improving enzyme robustness based on coevolutionary analysis and multidimensional virtual screening. Chem Sci 2024:d4sc02058h. [PMID: 39257856 PMCID: PMC11382147 DOI: 10.1039/d4sc02058h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/27/2024] [Indexed: 09/12/2024]  Open
7
Wang N, Zang ZH, Sun BB, Li B, Tian JL. Recent advances in computational prediction of molecular properties in food chemistry. Food Res Int 2024;192:114776. [PMID: 39147479 DOI: 10.1016/j.foodres.2024.114776] [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: 04/10/2024] [Revised: 07/10/2024] [Accepted: 07/14/2024] [Indexed: 08/17/2024]
8
Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024;20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [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: 01/31/2024]
9
Li J, Wang L, Zhu Z, Song C. Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. J Chem Inf Model 2024;64:301-315. [PMID: 38117138 PMCID: PMC10777399 DOI: 10.1021/acs.jcim.3c01381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
10
Colombo G. Computing allostery: from the understanding of biomolecular regulation and the discovery of cryptic sites to molecular design. Curr Opin Struct Biol 2023;83:102702. [PMID: 37716095 DOI: 10.1016/j.sbi.2023.102702] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
11
Yuan Y, Deng J, Cui Q. Molecular Dynamics Simulations Establish the Molecular Basis for the Broad Allostery Hotspot Distributions in the Tetracycline Repressor. J Am Chem Soc 2022;144:10870-10887. [PMID: 35675441 DOI: 10.1021/jacs.2c03275] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
12
van Keulen SC, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Hellgren Kotaleski J, Wade RC, Carloni P. Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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