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For: Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Protein folding problem: enigma, paradox, solution. Biophys Rev 2022;14:1255-1272. [PMID: 36659994 PMCID: PMC9842845 DOI: 10.1007/s12551-022-01000-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023]  Open
Number Cited by Other Article(s)
1
Recoulat Angelini AA, Malacrida L, González Flecha FL. Fluorescence phasor analysis: basic principles and biophysical applications. Biophys Rev 2025;17:395-408. [PMID: 40376409 PMCID: PMC12075720 DOI: 10.1007/s12551-025-01293-y] [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: 12/11/2024] [Accepted: 02/20/2025] [Indexed: 05/18/2025]  Open
2
Garbuzynskiy SO, Marchenkov VV, Marchenko NY, Semisotnov GV, Finkelstein AV. How proteins manage to fold and how chaperones manage to assist the folding. Phys Life Rev 2025;52:66-79. [PMID: 39709754 DOI: 10.1016/j.plrev.2024.12.006] [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: 12/06/2024] [Accepted: 12/12/2024] [Indexed: 12/24/2024]
3
Szczepski K, Jaremko Ł. AlphaFold and what is next: bridging functional, systems and structural biology. Expert Rev Proteomics 2025;22:45-58. [PMID: 39824781 DOI: 10.1080/14789450.2025.2456046] [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: 11/22/2024] [Revised: 01/13/2025] [Accepted: 01/16/2025] [Indexed: 01/20/2025]
4
Temussi PA, Martin SR, Pastore A. Life and death of Yfh1: how cool is cold denaturation. Q Rev Biophys 2025;58:e2. [PMID: 39801016 DOI: 10.1017/s0033583524000180] [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] [Indexed: 03/11/2025]
5
Strieder Philippsen G, Augusto Vicente Seixas F. Computational approach based on freely accessible tools for antimicrobial drug design. Bioorg Med Chem Lett 2025;115:130010. [PMID: 39486485 DOI: 10.1016/j.bmcl.2024.130010] [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: 08/05/2024] [Revised: 10/15/2024] [Accepted: 10/28/2024] [Indexed: 11/04/2024]
6
Kocher CD, Dill KA. Origins of Life: The Protein Folding Problem all over again? Proc Natl Acad Sci U S A 2024;121:e2315000121. [PMID: 39133848 PMCID: PMC11348307 DOI: 10.1073/pnas.2315000121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]  Open
7
Saha US, Vendruscolo M, Carpenter AE, Singh S, Bender A, Seal S. Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601740. [PMID: 39005404 PMCID: PMC11245006 DOI: 10.1101/2024.07.02.601740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
8
Fersht AR. From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding. Q Rev Biophys 2024;57:e4. [PMID: 38597675 DOI: 10.1017/s0033583523000045] [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] [Indexed: 04/11/2024]
9
Sun Y, Zhang F, Ouyang Q, Luo C. The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model. iScience 2024;27:109142. [PMID: 38384832 PMCID: PMC10879701 DOI: 10.1016/j.isci.2024.109142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024]  Open
10
Jahn R, Cafiso DC, Tamm LK. Mechanisms of SNARE proteins in membrane fusion. Nat Rev Mol Cell Biol 2024;25:101-118. [PMID: 37848589 PMCID: PMC11578640 DOI: 10.1038/s41580-023-00668-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/19/2023]
11
Turina P, Fariselli P, Capriotti E. K-Pro: Kinetics Data on Proteins and Mutants. J Mol Biol 2023;435:168245. [PMID: 37625584 DOI: 10.1016/j.jmb.2023.168245] [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: 02/14/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
12
Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023;24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [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: 08/17/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
13
Vila JA. Protein folding rate evolution upon mutations. Biophys Rev 2023;15:661-669. [PMID: 37681091 PMCID: PMC10480377 DOI: 10.1007/s12551-023-01088-z] [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: 04/10/2023] [Accepted: 06/24/2023] [Indexed: 09/09/2023]  Open
14
Sahakyan H, Nazaryan K, Mushegian A, Sorokina I. A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations. Int J Mol Sci 2023;24:10049. [PMID: 37373197 DOI: 10.3390/ijms241210049] [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: 05/13/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]  Open
15
Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Clarification to "Protein folding problem: enigma, paradox, solution". Biophys Rev 2023;15:161. [PMID: 37124919 PMCID: PMC10133415 DOI: 10.1007/s12551-023-01058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]  Open
16
Hall D. Biophysical Reviews: And the winner is …. Biophys Rev 2023;15:145-149. [PMID: 37124920 PMCID: PMC10133413 DOI: 10.1007/s12551-023-01062-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/02/2023]  Open
17
Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023;28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [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: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]  Open
18
Hall D. Biophysical Reviews: Turning the page from 2022 to 2023. Biophys Rev 2023;15:1-11. [PMID: 36909962 PMCID: PMC9995637 DOI: 10.1007/s12551-023-01049-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2023] [Indexed: 02/25/2023]  Open
19
Hall D, Basu G, Ito N. Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophys Rev 2022;14:1211-1222. [PMID: 36620377 PMCID: PMC9809522 DOI: 10.1007/s12551-022-01039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/05/2023]  Open
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