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For: Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics 2013;29:2722-8. [PMID: 23986568 PMCID: PMC3799472 DOI: 10.1093/bioinformatics/btt473] [Citation(s) in RCA: 625] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
Number Cited by Other Article(s)
1
Liu J, Neupane P, Cheng J. Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16. Proteins 2025. [PMID: 40452318 DOI: 10.1002/prot.26850] [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: 03/09/2025] [Revised: 05/06/2025] [Accepted: 05/23/2025] [Indexed: 06/11/2025]
2
Dumas N, Portelli G, Ji Y, Dupont F, Jendoubi M, Lalli E. Detection of protein structural hotspots using AI distillation and explainability: application to the DAX-1 protein. NAR Genom Bioinform 2025;7:lqaf047. [PMID: 40264682 PMCID: PMC12012785 DOI: 10.1093/nargab/lqaf047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 03/26/2025] [Accepted: 04/10/2025] [Indexed: 04/24/2025]  Open
3
d'Errico A, Vonk PJ, Wösten HAB, Lugones LG. Transposition of a non-autonomous element into the Gβ gene of Schizophyllum commune causes the streak mutation. Fungal Genet Biol 2025;179:104007. [PMID: 40447071 DOI: 10.1016/j.fgb.2025.104007] [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: 03/31/2025] [Revised: 05/21/2025] [Accepted: 05/24/2025] [Indexed: 06/11/2025]
4
Dennler O, Ryan CJ. Evaluating sequence and structural similarity metrics for predicting shared paralog functions. NAR Genom Bioinform 2025;7:lqaf051. [PMID: 40290317 PMCID: PMC12034104 DOI: 10.1093/nargab/lqaf051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 03/07/2025] [Accepted: 04/15/2025] [Indexed: 04/30/2025]  Open
5
Ma Z, Yang J. DeepUSPS: Deep Learning-Empowered Unconstrained-Structural Protein Sequence Design. Proteins 2025. [PMID: 40448386 DOI: 10.1002/prot.26847] [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: 01/08/2025] [Revised: 04/23/2025] [Accepted: 05/16/2025] [Indexed: 06/02/2025]
6
Techasen A, Worasith C, Muengsaen D, Ponglong J, Mahalapbutr P, Kongtaworn N, Rungrotmongkol T, Khongsukwiwat K, Wongphutorn P, Wangboon C, Homwonk C, Chaiyadet S, Laha T, Suttiprapa S, Sakonsinsiri C, Sithithaworn P, Thanan R. Identification and characterization of a target antigen recognized by the monoclonal antibody against Opisthorchis viverrini. PLoS One 2025;20:e0324137. [PMID: 40440420 PMCID: PMC12121735 DOI: 10.1371/journal.pone.0324137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 04/22/2025] [Indexed: 06/02/2025]  Open
7
Macdonald JR, Arnold MS, Luth MR, Cihalova D, Quinn RJ, Winzeler EA, Lee MC, van Dooren GG, Maier AG, Skinner-Adams TS, Andrews KT, Fisher GM. Inner-mitochondrial membrane protein PfMPV17 is linked to P. falciparum in vitro resistance to the indoloquinolizidine alkaloid alstonine. J Antimicrob Chemother 2025:dkaf141. [PMID: 40432501 DOI: 10.1093/jac/dkaf141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 04/27/2025] [Indexed: 05/29/2025]  Open
8
Harmalkar A, Lyskov S, Gray JJ. Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange. eLife 2025;13:RP94029. [PMID: 40424178 PMCID: PMC12113263 DOI: 10.7554/elife.94029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2025]  Open
9
Lin X, Chen Z, Li Y, Ma Z, Fan C, Cao Z, Feng S, Zhang J, Gao YQ. Unifying sequence-structure coding for advanced protein engineering via a multimodal diffusion transformer. Chem Sci 2025:d5sc02055g. [PMID: 40417294 PMCID: PMC12096517 DOI: 10.1039/d5sc02055g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2025] [Accepted: 05/14/2025] [Indexed: 05/27/2025]  Open
10
Balasco N, Modjtahedi N, Monti A, Ruvo M, Vitagliano L, Doti N. CHCHD4 Oxidoreductase Activity: A Comprehensive Analysis of the Molecular, Functional, and Structural Properties of Its Redox-Regulated Substrates. Molecules 2025;30:2117. [PMID: 40430290 PMCID: PMC12114033 DOI: 10.3390/molecules30102117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2025] [Revised: 04/24/2025] [Accepted: 05/06/2025] [Indexed: 05/29/2025]  Open
11
Dos Santos TG, Melgarejo AS, Ligabue-Braun R, de Oliveira DL. Phylogenetic and Structural Analyses of Vesicular Glutamate Transporters. Mol Neurobiol 2025:10.1007/s12035-025-05012-2. [PMID: 40338457 DOI: 10.1007/s12035-025-05012-2] [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: 10/01/2024] [Accepted: 04/29/2025] [Indexed: 05/09/2025]
12
Balasco N, Esposito L, Vitagliano L. Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code? Biomolecules 2025;15:674. [PMID: 40427567 PMCID: PMC12109453 DOI: 10.3390/biom15050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2025] [Revised: 04/24/2025] [Accepted: 05/02/2025] [Indexed: 05/29/2025]  Open
13
Maity D, Qiao B. AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools. ACS OMEGA 2025;10:17973-17982. [PMID: 40352555 PMCID: PMC12059942 DOI: 10.1021/acsomega.5c01263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 04/14/2025] [Accepted: 04/17/2025] [Indexed: 05/14/2025]
14
Raghuraman P, Park S. Exploring the modulation of phosphorylation and SUMOylation-dependent NPR1 conformational switching on immune regulators TGA3 and WRKY70 through molecular simulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025;222:109711. [PMID: 40056739 DOI: 10.1016/j.plaphy.2025.109711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 02/12/2025] [Accepted: 02/24/2025] [Indexed: 03/10/2025]
15
Jia F, Wang Y, Chen Z, Jin J, Zeng L, Zhang L, Tang H, Wang Y, Fan P. 10-Hydroxydec-2-enoic acid reduces vascular smooth muscle cell inflammation via interacting with Toll-like receptor 4. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2025;140:156534. [PMID: 40054182 DOI: 10.1016/j.phymed.2025.156534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 01/09/2025] [Accepted: 02/15/2025] [Indexed: 03/25/2025]
16
Kim TD, Pretorius D, Murray JW, Cardona T. Exploring the Structural Diversity and Evolution of the D1 Subunit of Photosystem II Using AlphaFold and Foldtree. PHYSIOLOGIA PLANTARUM 2025;177:e70284. [PMID: 40401773 PMCID: PMC12096807 DOI: 10.1111/ppl.70284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 04/24/2025] [Accepted: 04/29/2025] [Indexed: 05/23/2025]
17
Ragucci S, Campanile MG, Russo V, Landi N, Hussain HZF, Canonico E, Russo R, Russo M, Arcella A, Chambery A, Di Maro A. Hortensin 4, main type 1 ribosome inactivating protein from red mountain spinach seeds: Structural characterization and biological action. Int J Biol Macromol 2025;307:142085. [PMID: 40086539 DOI: 10.1016/j.ijbiomac.2025.142085] [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: 01/23/2025] [Revised: 03/07/2025] [Accepted: 03/12/2025] [Indexed: 03/16/2025]
18
dos Santos IC, de Souza RDS, Tolstoy I, Oliveira LS, Gruber A. Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels. Viruses 2025;17:642. [PMID: 40431654 PMCID: PMC12115509 DOI: 10.3390/v17050642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2025] [Revised: 04/23/2025] [Accepted: 04/25/2025] [Indexed: 05/29/2025]  Open
19
Walker DR, Fujimura G, Vanegas JM, Barbar EJ. Successful prediction of LC8 binding to intrinsically disordered proteins sheds light on AlphaFold's black box. Front Mol Biosci 2025;12:1531793. [PMID: 40337642 PMCID: PMC12057147 DOI: 10.3389/fmolb.2025.1531793] [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: 11/20/2024] [Accepted: 02/24/2025] [Indexed: 05/09/2025]  Open
20
Yan L, Zhang Q, Liu D, Zhao W, Yu Z. Identification and molecular mechanism of novel salt-enhancing peptide in crocodile hemoglobin: a combined E-tongue, molecular docking, and dynamic simulation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2025. [PMID: 40251916 DOI: 10.1002/jsfa.14289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2025] [Revised: 02/28/2025] [Accepted: 03/28/2025] [Indexed: 04/21/2025]
21
Liu J, Neupane P, Cheng J. Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.06.641913. [PMID: 40161604 PMCID: PMC11952293 DOI: 10.1101/2025.03.06.641913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
22
Rennie ML, Oliver MR. Emerging frontiers in protein structure prediction following the AlphaFold revolution. J R Soc Interface 2025;22:20240886. [PMID: 40233800 PMCID: PMC11999738 DOI: 10.1098/rsif.2024.0886] [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: 12/12/2024] [Revised: 02/04/2025] [Accepted: 03/10/2025] [Indexed: 04/17/2025]  Open
23
Wlodawer A, Dauter Z, Rubach P, Minor W, Jaskolski M, Jiang Z, Jeffcott W, Anosova O, Kurlin V. Duplicate entries in the Protein Data Bank: how to detect and handle them. Acta Crystallogr D Struct Biol 2025;81:170-180. [PMID: 40056147 PMCID: PMC11966240 DOI: 10.1107/s2059798325001883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Accepted: 02/27/2025] [Indexed: 03/10/2025]  Open
24
Wali MH, Naif HM, Abdul Rahim NA, Yunus MA. Genetic Diversity in the Fusion Gene of Respiratory Syncytial Virus (RSV) Isolated From Iraqi Patients: A First Report. Adv Virol 2025;2025:8864776. [PMID: 40191805 PMCID: PMC11971507 DOI: 10.1155/av/8864776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 03/08/2025] [Indexed: 04/09/2025]  Open
25
Santos TNF, Moreira RO, Rodrigues JDB, Rojas LAC, Souza JAM, Desidério JA. Isolation and in silico analysis of a new subclass of parasporin 4 from Bacillus thuringiensis coreanensis. PeerJ 2025;13:e19061. [PMID: 40151459 PMCID: PMC11949118 DOI: 10.7717/peerj.19061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Accepted: 02/06/2025] [Indexed: 03/29/2025]  Open
26
Rodríguez-Fernández MA, Tristán-Flores FE, Casique-Aguirre D, Negrete-Rodríguez MDLLX, Cervantes-Montelongo JA, Conde-Barajas E, Acosta-García G, Silva-Martínez GA. Virtual Screening and Molecular Dynamics of Cytokine-Drug Complexes for Atherosclerosis Therapy. Int J Mol Sci 2025;26:2931. [PMID: 40243563 PMCID: PMC11988346 DOI: 10.3390/ijms26072931] [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: 03/01/2025] [Revised: 03/19/2025] [Accepted: 03/21/2025] [Indexed: 04/18/2025]  Open
27
Li XZ, Li YL, Zhu JS. Three-Dimensional Structural Heteromorphs of Mating-Type Proteins in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungal Complex. J Fungi (Basel) 2025;11:244. [PMID: 40278065 PMCID: PMC12028455 DOI: 10.3390/jof11040244] [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: 01/13/2025] [Revised: 02/21/2025] [Accepted: 03/18/2025] [Indexed: 04/26/2025]  Open
28
Spanke VA, Egger-Hoerschinger VJ, Ruzsanyi V, Liedl KR. From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4. J Comput Aided Mol Des 2025;39:12. [PMID: 40095179 PMCID: PMC11913904 DOI: 10.1007/s10822-025-00589-1] [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: 09/18/2024] [Accepted: 03/01/2025] [Indexed: 03/19/2025]
29
Xing E, Zhang J, Wang S, Cheng X. Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2. RESEARCH SQUARE 2025:rs.3.rs-6087969. [PMID: 40092441 PMCID: PMC11908349 DOI: 10.21203/rs.3.rs-6087969/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
30
Han B, Zhang Y, Li L, Gong X, Xia K. TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment. Brief Bioinform 2025;26:bbaf083. [PMID: 40062613 PMCID: PMC11891663 DOI: 10.1093/bib/bbaf083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 01/11/2025] [Accepted: 02/17/2025] [Indexed: 05/13/2025]  Open
31
Quast NP, Abanades B, Guloglu B, Karuppiah V, Harper S, Raybould MIJ, Deane CM. T-cell receptor structures and predictive models reveal comparable alpha and beta chain structural diversity despite differing genetic complexity. Commun Biol 2025;8:362. [PMID: 40038394 PMCID: PMC11880327 DOI: 10.1038/s42003-025-07708-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 02/09/2025] [Indexed: 03/06/2025]  Open
32
Feldman J, Skolnick J. AF3Complex Yields Improved Structural Predictions of Protein Complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.27.640585. [PMID: 40093092 PMCID: PMC11908126 DOI: 10.1101/2025.02.27.640585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
33
Kim G, Lee S, Levy Karin E, Kim H, Moriwaki Y, Ovchinnikov S, Steinegger M, Mirdita M. Easy and accurate protein structure prediction using ColabFold. Nat Protoc 2025;20:620-642. [PMID: 39402428 DOI: 10.1038/s41596-024-01060-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 08/07/2024] [Indexed: 03/12/2025]
34
Jung N, Vellozo-Echevarría T, Barrett K, Meyer AS. Analysis of enzyme kinetics of fungal methionine synthases in an optimized colorimetric microscale assay for measuring cobalamin-independent methionine synthase activity. Enzyme Microb Technol 2025;184:110581. [PMID: 39824044 DOI: 10.1016/j.enzmictec.2025.110581] [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: 11/18/2024] [Revised: 01/01/2025] [Accepted: 01/02/2025] [Indexed: 01/20/2025]
35
Vangaru S, Bhattacharya D. To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.22.639681. [PMID: 40060396 PMCID: PMC11888329 DOI: 10.1101/2025.02.22.639681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
36
Kumar BH, Kabekkodu SP, Pai KSR. Structural insights of AKT and its activation mechanism for drug development. Mol Divers 2025:10.1007/s11030-025-11132-7. [PMID: 40009150 DOI: 10.1007/s11030-025-11132-7] [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: 01/07/2025] [Accepted: 02/09/2025] [Indexed: 02/27/2025]
37
Zhou L, Ortega-Rodriguez U, Flores MJ, Matsumoto Y, Bettinger JQ, Wu WW, Zhang Y, Kim SR, Biel TG, Pritts JD, Shen RF, Rao VA, Ju T. Dual functional POGases from bacteria encompassing broader O-glycanase and adhesin activities. Nat Commun 2025;16:1960. [PMID: 40000644 PMCID: PMC11861894 DOI: 10.1038/s41467-025-57143-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 02/11/2025] [Indexed: 02/27/2025]  Open
38
Maisuradze GG, Thakur A, Khatri K, Haldane A, Levy RM. Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.637534. [PMID: 39990457 PMCID: PMC11844428 DOI: 10.1101/2025.02.10.637534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
39
Tauriello G, Waterhouse AM, Haas J, Behringer D, Bienert S, Garello T, Schwede T. ModelArchive: A Deposition Database for Computational Macromolecular Structural Models. J Mol Biol 2025:168996. [PMID: 39947281 DOI: 10.1016/j.jmb.2025.168996] [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: 11/30/2024] [Revised: 02/04/2025] [Accepted: 02/07/2025] [Indexed: 02/27/2025]
40
Ghodrati F, Parivar K, Amiri I, Roodbari NH. Exploring miR-34a, miR-449, and ADAM2/ADAM7 Expressions as Potential Biomarkers in Male Infertility: A Combined In Silico and Experimental Approach. Biochem Genet 2025:10.1007/s10528-025-11050-1. [PMID: 39928278 DOI: 10.1007/s10528-025-11050-1] [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: 12/04/2024] [Accepted: 01/31/2025] [Indexed: 02/11/2025]
41
Morehead A, Giri N, Liu J, Neupane P, Cheng J. Deep Learning for Protein-Ligand Docking: Are We There Yet? ARXIV 2025:arXiv:2405.14108v5. [PMID: 38827451 PMCID: PMC11142318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
42
Banna HA, Berg K, Sadat T, Das N, Paudel R, D'Souza V, Koirala D. Synthetic anti-RNA antibody derivatives for RNA visualization in mammalian cells. Nucleic Acids Res 2025;53:gkae1275. [PMID: 39739875 PMCID: PMC11879077 DOI: 10.1093/nar/gkae1275] [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: 04/17/2024] [Revised: 11/15/2024] [Accepted: 12/12/2024] [Indexed: 01/02/2025]  Open
43
Vincenzi M, Mercurio FA, Autiero I, Leone M. Sam-Sam Association Between EphA2 and SASH1: In Silico Studies of Cancer-Linked Mutations. Molecules 2025;30:718. [PMID: 39942820 PMCID: PMC11820823 DOI: 10.3390/molecules30030718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2024] [Revised: 01/21/2025] [Accepted: 01/30/2025] [Indexed: 02/16/2025]  Open
44
Zhou Z, Riley R, Kautsar S, Wu W, Egan R, Hofmeyr S, Goldhaber-Gordon S, Yu M, Ho H, Liu F, Chen F, Morgan-Kiss R, Shi L, Liu H, Wang Z. GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.30.635558. [PMID: 39975405 PMCID: PMC11838515 DOI: 10.1101/2025.01.30.635558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
45
Prabakaran R, Bromberg Y. Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools. Bioinformatics 2025;41:btaf035. [PMID: 39854283 PMCID: PMC11821270 DOI: 10.1093/bioinformatics/btaf035] [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: 07/17/2024] [Revised: 11/04/2024] [Accepted: 01/22/2025] [Indexed: 01/26/2025]  Open
46
Wang M, Robertson D, Zou J, Spanos C, Rappsilber J, Marston AL. Molecular mechanism targeting condensin for chromosome condensation. EMBO J 2025;44:705-735. [PMID: 39690240 PMCID: PMC11791182 DOI: 10.1038/s44318-024-00336-6] [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] [Received: 05/22/2024] [Revised: 11/26/2024] [Accepted: 12/02/2024] [Indexed: 12/19/2024]  Open
47
Mi T, Xiao N, Gong H. GDFold2: A fast and parallelizable protein folding environment with freely defined objective functions. Protein Sci 2025;34:e70041. [PMID: 39873342 PMCID: PMC11773392 DOI: 10.1002/pro.70041] [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: 08/28/2024] [Revised: 12/31/2024] [Accepted: 01/10/2025] [Indexed: 01/30/2025]
48
Simpson J, Kasson PM. Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses. PLoS Comput Biol 2025;21:e1012812. [PMID: 39908344 PMCID: PMC11809852 DOI: 10.1371/journal.pcbi.1012812] [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: 10/01/2024] [Revised: 02/10/2025] [Accepted: 01/20/2025] [Indexed: 02/07/2025]  Open
49
Dey M, Gupta A, Badmalia MD, Ashish, Sharma D. Visualizing gaussian-chain like structural models of human α-synuclein in monomeric pre-fibrillar state: Solution SAXS data and modeling analysis. Int J Biol Macromol 2025;288:138614. [PMID: 39674478 DOI: 10.1016/j.ijbiomac.2024.138614] [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: 07/23/2024] [Revised: 12/08/2024] [Accepted: 12/08/2024] [Indexed: 12/16/2024]
50
Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Żyła A, Westhof E, Miao Z. RNA-Puzzles Round V: blind predictions of 23 RNA structures. Nat Methods 2025;22:399-411. [PMID: 39623050 PMCID: PMC11810798 DOI: 10.1038/s41592-024-02543-9] [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: 02/15/2024] [Accepted: 10/29/2024] [Indexed: 01/16/2025]
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