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For: Wallner B. AFsample: improving multimer prediction with AlphaFold using massive sampling. Bioinformatics 2023;39:btad573. [PMID: 37713472 PMCID: PMC10534052 DOI: 10.1093/bioinformatics/btad573] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/29/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023]  Open
Number Cited by Other Article(s)
1
O'Donnell TJ, Kanduri C, Isacchini G, Limenitakis JP, Brachman RA, Alvarez RA, Haff IH, Sandve GK, Greiff V. Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning. Cell Syst 2024;15:1168-1189. [PMID: 39701034 DOI: 10.1016/j.cels.2024.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/16/2024] [Accepted: 11/14/2024] [Indexed: 12/21/2024]
2
Li C, Luo Y, Xie Y, Zhang Z, Liu Y, Zou L, Xiao F. Structural and functional prediction, evaluation, and validation in the post-sequencing era. Comput Struct Biotechnol J 2024;23:446-451. [PMID: 38223342 PMCID: PMC10787220 DOI: 10.1016/j.csbj.2023.12.031] [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: 10/20/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024]  Open
3
Lazou M, Khan O, Nguyen T, Padhorny D, Kozakov D, Joseph-McCarthy D, Vajda S. Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much. Proc Natl Acad Sci U S A 2024;121:e2412719121. [PMID: 39565312 PMCID: PMC11621821 DOI: 10.1073/pnas.2412719121] [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: 06/24/2024] [Accepted: 10/21/2024] [Indexed: 11/21/2024]  Open
4
Wu D, Yin R, Chen G, Ribeiro-Filho HV, Cheung M, Robbins PF, Mariuzza RA, Pierce BG. Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens. SCIENCE ADVANCES 2024;10:eadq6150. [PMID: 39576860 PMCID: PMC11584006 DOI: 10.1126/sciadv.adq6150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 10/21/2024] [Indexed: 11/24/2024]
5
Yudenko A, Bukhdruker S, Shishkin P, Rodin S, Burtseva A, Petrov A, Pigareva N, Sokolov A, Zinovev E, Eliseev I, Remeeva A, Marin E, Mishin A, Gordeliy V, Gushchin I, Ischenko A, Borshchevskiy V. Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers. Structure 2024:S0969-2126(24)00463-5. [PMID: 39566503 DOI: 10.1016/j.str.2024.10.028] [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: 08/02/2024] [Revised: 09/16/2024] [Accepted: 10/24/2024] [Indexed: 11/22/2024]
6
Raouraoua N, Mirabello C, Véry T, Blanchet C, Wallner B, Lensink MF, Brysbaert G. MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling. NATURE COMPUTATIONAL SCIENCE 2024;4:824-828. [PMID: 39528570 PMCID: PMC11578886 DOI: 10.1038/s43588-024-00714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 10/03/2024] [Indexed: 11/16/2024]
7
McFee M, Kim J, Kim PM. EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces. Bioinformatics 2024;40:btae636. [PMID: 39441796 PMCID: PMC11543620 DOI: 10.1093/bioinformatics/btae636] [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: 06/07/2024] [Revised: 10/16/2024] [Accepted: 10/21/2024] [Indexed: 10/25/2024]  Open
8
Xu J, Wang Y. Generating Multistate Conformations of P-type ATPases with a Conditional Diffusion Model. J Chem Inf Model 2024. [PMID: 39480276 DOI: 10.1021/acs.jcim.4c01519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
9
Büttiker P, Boukherissa A, Weissenberger S, Ptacek R, Anders M, Raboch J, Stefano GB. Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods. Cell Mol Neurobiol 2024;44:72. [PMID: 39467848 PMCID: PMC11519248 DOI: 10.1007/s10571-024-01509-x] [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: 09/02/2024] [Accepted: 10/22/2024] [Indexed: 10/30/2024]
10
Bellinzona G, Sassera D, Bonvin AMJJ. Accelerating protein-protein interaction screens with reduced AlphaFold-Multimer sampling. BIOINFORMATICS ADVANCES 2024;4:vbae153. [PMID: 39464748 PMCID: PMC11513016 DOI: 10.1093/bioadv/vbae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/30/2024] [Accepted: 10/10/2024] [Indexed: 10/29/2024]
11
Mirabello C, Wallner B, Nystedt B, Azinas S, Carroni M. Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes. Nat Commun 2024;15:8724. [PMID: 39379372 PMCID: PMC11461844 DOI: 10.1038/s41467-024-52951-w] [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: 05/13/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024]  Open
12
Träger TK, Tüting C, Kastritis PL. The human touch: Utilizing AlphaFold 3 to analyze structures of endogenous metabolons. Structure 2024;32:1555-1562. [PMID: 39303718 DOI: 10.1016/j.str.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 08/26/2024] [Indexed: 09/22/2024]
13
Rosignoli S, Pacelli M, Manganiello F, Paiardini A. An outlook on structural biology after AlphaFold: tools, limits and perspectives. FEBS Open Bio 2024. [PMID: 39313455 DOI: 10.1002/2211-5463.13902] [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: 03/13/2024] [Revised: 08/19/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024]  Open
14
Benavides TL, Montelione GT. Integrative Modeling of Protein-Polypeptide Complexes by Bayesian Model Selection using AlphaFold and NMR Chemical Shift Perturbation Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613999. [PMID: 39345459 PMCID: PMC11430059 DOI: 10.1101/2024.09.19.613999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
15
Liu J, Guo Z, You H, Zhang C, Lai L. All-Atom Protein Sequence Design Based on Geometric Deep Learning. Angew Chem Int Ed Engl 2024:e202411461. [PMID: 39295564 DOI: 10.1002/anie.202411461] [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: 06/18/2024] [Revised: 09/09/2024] [Accepted: 09/18/2024] [Indexed: 09/21/2024]
16
Stahl K, Warneke R, Demann L, Bremenkamp R, Hormes B, Brock O, Stülke J, Rappsilber J. Modelling protein complexes with crosslinking mass spectrometry and deep learning. Nat Commun 2024;15:7866. [PMID: 39251624 PMCID: PMC11383924 DOI: 10.1038/s41467-024-51771-2] [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: 09/08/2023] [Accepted: 08/16/2024] [Indexed: 09/11/2024]  Open
17
Xing C, Li G, Zheng X, Li P, Yuan J, Yan W. Characterization of a Novel Monoclonal Antibody with High Affinity and Specificity against Aflatoxins: A Discovery from Rosetta Antibody-Ligand Computational Simulation. J Chem Inf Model 2024;64:6814-6826. [PMID: 39157865 DOI: 10.1021/acs.jcim.4c00736] [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: 08/20/2024]
18
Guzmán-Vega FJ, Arold ST. AlphaCRV: a pipeline for identifying accurate binder topologies in mass-modeling with AlphaFold. BIOINFORMATICS ADVANCES 2024;4:vbae131. [PMID: 39286602 PMCID: PMC11405088 DOI: 10.1093/bioadv/vbae131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/05/2024] [Accepted: 09/04/2024] [Indexed: 09/19/2024]
19
Konold PE, Monrroy L, Bellisario A, Filipe D, Adams P, Alvarez R, Bean R, Bielecki J, Bódizs S, Ducrocq G, Grubmueller H, Kirian RA, Kloos M, Koliyadu JCP, Koua FHM, Larkiala T, Letrun R, Lindsten F, Maihöfer M, Martin AV, Mészáros P, Mutisya J, Nimmrich A, Okamoto K, Round A, Sato T, Valerio J, Westphal D, Wollter A, Yenupuri TV, You T, Maia F, Westenhoff S. Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs. Nat Methods 2024;21:1608-1611. [PMID: 38969722 PMCID: PMC11399097 DOI: 10.1038/s41592-024-02344-0] [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: 11/20/2023] [Accepted: 06/10/2024] [Indexed: 07/07/2024]
20
Bryant P, Noé F. Structure prediction of alternative protein conformations. Nat Commun 2024;15:7328. [PMID: 39187507 PMCID: PMC11347660 DOI: 10.1038/s41467-024-51507-2] [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: 10/11/2023] [Accepted: 08/07/2024] [Indexed: 08/28/2024]  Open
21
Edmunds NS, Genc AG, McGuffin LJ. Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes. Bioinformatics 2024;40:btae491. [PMID: 39115813 PMCID: PMC11322044 DOI: 10.1093/bioinformatics/btae491] [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: 05/25/2024] [Revised: 07/09/2024] [Indexed: 08/15/2024]  Open
22
Agarwal V, McShan AC. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins. Nat Chem Biol 2024;20:950-959. [PMID: 38907110 DOI: 10.1038/s41589-024-01638-w] [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: 05/22/2023] [Accepted: 04/29/2024] [Indexed: 06/23/2024]
23
Shor B, Schneidman-Duhovny D. Integrative modeling meets deep learning: Recent advances in modeling protein assemblies. Curr Opin Struct Biol 2024;87:102841. [PMID: 38795564 DOI: 10.1016/j.sbi.2024.102841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/28/2024]
24
Swapna GVT, Dube N, Roth MJ, Montelione GT. Modeling Alternative Conformational States of Pseudo-Symmetric Solute Carrier Transporters using Methods from Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603529. [PMID: 39071413 PMCID: PMC11275918 DOI: 10.1101/2024.07.15.603529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
25
Bryant P, Noé F. Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile. PLoS Comput Biol 2024;20:e1012253. [PMID: 39052676 DOI: 10.1371/journal.pcbi.1012253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 08/06/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024]  Open
26
McLean TC. LazyAF, a pipeline for accessible medium-scale in silico prediction of protein-protein interactions. MICROBIOLOGY (READING, ENGLAND) 2024;170:001473. [PMID: 38967642 PMCID: PMC11316561 DOI: 10.1099/mic.0.001473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024]
27
Huang YJ, Montelione GT. Hidden Structural States of Proteins Revealed by Conformer Selection with AlphaFold-NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.26.600902. [PMID: 38979209 PMCID: PMC11230435 DOI: 10.1101/2024.06.26.600902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
28
El Salamouni NS, Cater JH, Spenkelink LM, Yu H. Nanobody engineering: computational modelling and design for biomedical and therapeutic applications. FEBS Open Bio 2024. [PMID: 38898362 DOI: 10.1002/2211-5463.13850] [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: 04/05/2024] [Revised: 05/25/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]  Open
29
Urvas L, Chiesa L, Bret G, Jacquemard C, Kellenberger E. Benchmarking AlphaFold-Generated Structures of Chemokine-Chemokine Receptor Complexes. J Chem Inf Model 2024;64:4587-4600. [PMID: 38809680 DOI: 10.1021/acs.jcim.3c01835] [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: 05/31/2024]
30
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 2024;630:493-500. [PMID: 38718835 PMCID: PMC11168924 DOI: 10.1038/s41586-024-07487-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
31
Wu D, Yin R, Chen G, Ribeiro-Filho HV, Cheung M, Robbins PF, Mariuzza RA, Pierce BG. Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595215. [PMID: 38826362 PMCID: PMC11142219 DOI: 10.1101/2024.05.21.595215] [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]
32
Sonmez C, Toia B, Eickhoff P, Matei AM, El Beyrouthy M, Wallner B, Douglas ME, de Lange T, Lottersberger F. DNA-PK controls Apollo's access to leading-end telomeres. Nucleic Acids Res 2024;52:4313-4327. [PMID: 38407308 PMCID: PMC11077071 DOI: 10.1093/nar/gkae105] [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: 05/19/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 02/27/2024]  Open
33
Ellaway JIJ, Anyango S, Nair S, Zaki HA, Nadzirin N, Powell HR, Gutmanas A, Varadi M, Velankar S. Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024;11:034701. [PMID: 38774441 PMCID: PMC11106648 DOI: 10.1063/4.0000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024]
34
Schmid EW, Walter JC. Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588596. [PMID: 38645019 PMCID: PMC11030396 DOI: 10.1101/2024.04.09.588596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
35
Monteiro da Silva G, Cui JY, Dalgarno DC, Lisi GP, Rubenstein BM. High-throughput prediction of protein conformational distributions with subsampled AlphaFold2. Nat Commun 2024;15:2464. [PMID: 38538622 PMCID: PMC10973385 DOI: 10.1038/s41467-024-46715-9] [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: 08/03/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024]  Open
36
Jänes J, Beltrao P. Deep learning for protein structure prediction and design-progress and applications. Mol Syst Biol 2024;20:162-169. [PMID: 38291232 PMCID: PMC10912668 DOI: 10.1038/s44320-024-00016-x] [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: 06/26/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]  Open
37
Shor B, Schneidman-Duhovny D. CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2. Nat Methods 2024;21:477-487. [PMID: 38326495 PMCID: PMC10927564 DOI: 10.1038/s41592-024-02174-0] [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: 05/17/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
38
Chu AE, Lu T, Huang PS. Sparks of function by de novo protein design. Nat Biotechnol 2024;42:203-215. [PMID: 38361073 PMCID: PMC11366440 DOI: 10.1038/s41587-024-02133-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
39
Bret H, Gao J, Zea DJ, Andreani J, Guerois R. From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2. Nat Commun 2024;15:597. [PMID: 38238291 PMCID: PMC10796318 DOI: 10.1038/s41467-023-44288-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024]  Open
40
Yin R, Pierce BG. Evaluation of AlphaFold antibody-antigen modeling with implications for improving predictive accuracy. Protein Sci 2024;33:e4865. [PMID: 38073135 PMCID: PMC10751731 DOI: 10.1002/pro.4865] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
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Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez‐Lumbreras LA, Fernandez‐Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang S, Roel‐Touris J, Jimenez‐Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas‐Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman‐Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota‐Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda‐Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91:1658-1683. [PMID: 37905971 PMCID: PMC10841881 DOI: 10.1002/prot.26609] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
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Hou Y, Xie T, He L, Tao L, Huang J. Topological links in predicted protein complex structures reveal limitations of AlphaFold. Commun Biol 2023;6:1098. [PMID: 37898666 PMCID: PMC10613300 DOI: 10.1038/s42003-023-05489-4] [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: 02/21/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]  Open
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