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For: Raimondi D, Orlando G, Michiels E, Pakravan D, Bratek-Skicki A, Van Den Bosch L, Moreau Y, Rousseau F, Schymkowitz J. In-silico prediction of in-vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention. Bioinformatics 2021;37:3473-3479. [PMID: 33983381 DOI: 10.1093/bioinformatics/btab350] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/15/2021] [Accepted: 05/10/2021] [Indexed: 01/21/2023]  Open
Number Cited by Other Article(s)
1
Monti M, Fiorentino J, Miltiadis-Vrachnos D, Bini G, Cotrufo T, Sanchez de Groot N, Armaos A, Tartaglia GG. catGRANULE 2.0: accurate predictions of liquid-liquid phase separating proteins at single amino acid resolution. Genome Biol 2025;26:33. [PMID: 39979996 PMCID: PMC11843755 DOI: 10.1186/s13059-025-03497-7] [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: 07/19/2024] [Accepted: 02/06/2025] [Indexed: 02/22/2025]  Open
2
Ahmed Z, Shahzadi K, Jin Y, Li R, Momanyi BM, Zulfiqar H, Ning L, Lin H. Identification of RNA‐dependent liquid‐liquid phase separation proteins using an artificial intelligence strategy. Proteomics 2024;24:e2400044. [PMID: 38824664 DOI: 10.1002/pmic.202400044] [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: 01/26/2024] [Revised: 05/03/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
3
Frank M, Ni P, Jensen M, Gerstein MB. Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proc Natl Acad Sci U S A 2024;121:e2320510121. [PMID: 39110734 PMCID: PMC11331094 DOI: 10.1073/pnas.2320510121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/03/2024] [Indexed: 08/21/2024]  Open
4
Chin KY, Ishida S, Sasaki Y, Terayama K. Predicting condensate formation of protein and RNA under various environmental conditions. BMC Bioinformatics 2024;25:143. [PMID: 38566033 PMCID: PMC10988968 DOI: 10.1186/s12859-024-05764-z] [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: 12/01/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024]  Open
5
Deng B, Wan G. Technologies for studying phase-separated biomolecular condensates. ADVANCED BIOTECHNOLOGY 2024;2:10. [PMID: 39883284 PMCID: PMC11740866 DOI: 10.1007/s44307-024-00020-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 01/31/2025]
6
Liao S, Zhang Y, Han X, Wang T, Wang X, Yan Q, Li Q, Qi Y, Zhang Z. A sequence-based model for identifying proteins undergoing liquid-liquid phase separation/forming fibril aggregates via machine learning. Protein Sci 2024;33:e4927. [PMID: 38380794 PMCID: PMC10880426 DOI: 10.1002/pro.4927] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
7
Saar KL, Qian D, Good LL, Morgunov AS, Collepardo-Guevara R, Best RB, Knowles TPJ. Theoretical and Data-Driven Approaches for Biomolecular Condensates. Chem Rev 2023;123:8988-9009. [PMID: 37171907 PMCID: PMC10375482 DOI: 10.1021/acs.chemrev.2c00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 05/14/2023]
8
Nadendla K, Simpson GG, Becher J, Journeaux T, Cabeza-Cabrerizo M, Bernardes GJL. Strategies for Conditional Regulation of Proteins. JACS AU 2023;3:344-357. [PMID: 36873677 PMCID: PMC9975842 DOI: 10.1021/jacsau.2c00654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
9
Chew PY, Reinhardt A. Phase diagrams-Why they matter and how to predict them. J Chem Phys 2023;158:030902. [PMID: 36681642 DOI: 10.1063/5.0131028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
10
Roca-Martinez J, Lazar T, Gavalda-Garcia J, Bickel D, Pancsa R, Dixit B, Tzavella K, Ramasamy P, Sanchez-Fornaris M, Grau I, Vranken WF. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior. Front Mol Biosci 2022;9:959956. [PMID: 35992270 PMCID: PMC9382080 DOI: 10.3389/fmolb.2022.959956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]  Open
11
Orlando G, Raimondi D, Duran-Romaña R, Moreau Y, Schymkowitz J, Rousseau F. PyUUL provides an interface between biological structures and deep learning algorithms. Nat Commun 2022;13:961. [PMID: 35181656 PMCID: PMC8857184 DOI: 10.1038/s41467-022-28327-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/18/2022] [Indexed: 11/09/2022]  Open
12
Wang X, Zhou X, Yan Q, Liao S, Tang W, Xu P, Gao Y, Li Q, Dou Z, Yang W, Huang B, Li J, Zhang Z. LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro. Bioinformatics 2022;38:2010-2014. [PMID: 35025997 PMCID: PMC8963276 DOI: 10.1093/bioinformatics/btac026] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 11/14/2022]  Open
13
Lindorff-Larsen K, Kragelund BB. On the potential of machine learning to examine the relationship between sequence, structure, dynamics and function of intrinsically disordered proteins. J Mol Biol 2021;433:167196. [PMID: 34390736 DOI: 10.1016/j.jmb.2021.167196] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
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