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For: Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nat Commun 2021;12:1340. [PMID: 33637700 PMCID: PMC7910447 DOI: 10.1038/s41467-021-21511-x] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/18/2021] [Indexed: 11/22/2022]  Open
Number Cited by Other Article(s)
1
Mendes GEM, Maio AR, Oliveira GDSRD, Rosa LC, Carvalho Costa LD, Oliveira LCVD, Freitas MSD, Cordeiro E Silva R, Santos Galvao RMD, Coutinho RC, Rezende Santos TC, Souza Carvalho TD, Souza Lima VHD, Bello ML. Biomolecular conformational changes and transient druggable binding sites through full-length AMPK molecular dynamics simulations. J Mol Graph Model 2025;138:109039. [PMID: 40186940 DOI: 10.1016/j.jmgm.2025.109039] [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: 05/27/2024] [Revised: 03/16/2025] [Accepted: 03/26/2025] [Indexed: 04/07/2025]
2
Zhu H, Terashi G, Farheen F, Nakamura T, Kihara D. AI-based quality assessment methods for protein structure models from cryo-EM. Curr Res Struct Biol 2025;9:100164. [PMID: 39996138 PMCID: PMC11848767 DOI: 10.1016/j.crstbi.2025.100164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/23/2025] [Accepted: 01/29/2025] [Indexed: 02/26/2025]  Open
3
Maurino VG. Next generation technologies for protein structure determination: challenges and breakthroughs in plant biology applications. JOURNAL OF PLANT PHYSIOLOGY 2025;310:154522. [PMID: 40382917 DOI: 10.1016/j.jplph.2025.154522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2025] [Revised: 05/13/2025] [Accepted: 05/14/2025] [Indexed: 05/20/2025]
4
Cui X, Xia Y, Hou M, Zhao X, Wang S, Zhang G. M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling. BMC Bioinformatics 2025;26:120. [PMID: 40325375 PMCID: PMC12054043 DOI: 10.1186/s12859-025-06131-2] [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: 01/22/2024] [Accepted: 04/03/2025] [Indexed: 05/07/2025]  Open
5
Wang X, Zhang T, Liu G, Cui Z, Zeng Z, Long C, Zheng W, Yang J. LightRoseTTA: High-Efficient and Accurate Protein Structure Prediction Using a Light-Weight Deep Graph Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2309051. [PMID: 40134034 PMCID: PMC12097069 DOI: 10.1002/advs.202309051] [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: 11/23/2023] [Revised: 04/17/2024] [Indexed: 03/27/2025]
6
Li J, Chen X, Huang H, Zeng M, Yu J, Gong X, Ye Q. $\mathcal{S}$ able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm. Brief Bioinform 2025;26:bbaf120. [PMID: 40163822 PMCID: PMC11957296 DOI: 10.1093/bib/bbaf120] [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: 10/29/2024] [Revised: 01/23/2025] [Accepted: 02/23/2025] [Indexed: 04/02/2025]  Open
7
Yang W, Hicks DR, Ghosh A, Schwartze TA, Conventry B, Goreshnik I, Allen A, Halabiya SF, Kim CJ, Hinck CS, Lee DS, Bera AK, Li Z, Wang Y, Schlichthaerle T, Cao L, Huang B, Garrett S, Gerben SR, Rettie S, Heine P, Murray A, Edman N, Carter L, Stewart L, Almo SC, Hinck AP, Baker D. Design of high-affinity binders to immune modulating receptors for cancer immunotherapy. Nat Commun 2025;16:2001. [PMID: 40011465 PMCID: PMC11865580 DOI: 10.1038/s41467-025-57192-z] [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: 08/26/2024] [Accepted: 02/14/2025] [Indexed: 02/28/2025]  Open
8
Giberti S, Dutta S, Corni S, Frasconi M, Brancolini G. Protein-surface interactions in nano-scale biosensors for IL-6 detection using functional monolayers. NANOSCALE 2025;17:4389-4399. [PMID: 39831436 DOI: 10.1039/d4nr04199b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
9
Thorlacius A, Rulev M, Sundberg O, Sundborger-Lunna A. Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers. Commun Biol 2025;8:182. [PMID: 39910321 PMCID: PMC11799418 DOI: 10.1038/s42003-025-07610-1] [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: 08/26/2024] [Accepted: 01/27/2025] [Indexed: 02/07/2025]  Open
10
Wang H, Sun M, Xie L, Liu D, Zhang G. Physical-aware model accuracy estimation for protein complex using deep learning method. Comput Struct Biotechnol J 2025;27:478-487. [PMID: 39916698 PMCID: PMC11799971 DOI: 10.1016/j.csbj.2025.01.017] [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: 10/30/2024] [Revised: 01/18/2025] [Accepted: 01/21/2025] [Indexed: 02/09/2025]  Open
11
Wang W, Gong Z, Hendrickson WA. AlphaFold-guided molecular replacement for solving challenging crystal structures. Acta Crystallogr D Struct Biol 2025;81:4-21. [PMID: 39711199 PMCID: PMC11740581 DOI: 10.1107/s2059798324011999] [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: 11/08/2023] [Accepted: 12/11/2024] [Indexed: 12/24/2024]  Open
12
Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. Design of pseudosymmetric protein hetero-oligomers. Nat Commun 2024;15:10684. [PMID: 39695145 PMCID: PMC11655659 DOI: 10.1038/s41467-024-54913-8] [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: 07/20/2023] [Accepted: 11/20/2024] [Indexed: 12/20/2024]  Open
13
Liang F, Sun M, Xie L, Zhao X, Liu D, Zhao K, Zhang G. Recent advances and challenges in protein complex model accuracy estimation. Comput Struct Biotechnol J 2024;23:1824-1832. [PMID: 38707538 PMCID: PMC11066466 DOI: 10.1016/j.csbj.2024.04.049] [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: 01/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]  Open
14
Briones AC, Megino RF, Marin AV, Chacón-Arguedas D, García-Martinez E, Balastegui-Martín H, Reyburn HT, Henrickson SE, Rodríguez-Sainz C, Seoane-Reula E, Sanchez-Mateos P, Cardenas PP, Regueiro JR. Nonsense CD247 mutations show dominant-negative features in T-cell receptor expression and function. J Allergy Clin Immunol 2024;154:1022-1032. [PMID: 38992472 DOI: 10.1016/j.jaci.2024.06.019] [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: 01/04/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
15
Han S, Li C, Li M, Lenzen M, Chen X, Zhang Y, Li M, Yin T, Li Y, Li J, Liu J, Li Y. Prospects for global sustainable development through integrating the environmental impacts of economic activities. Nat Commun 2024;15:8424. [PMID: 39341803 PMCID: PMC11438875 DOI: 10.1038/s41467-024-52854-w] [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: 01/31/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]  Open
16
Anishchenko I, Kipnis Y, Kalvet I, Zhou G, Krishna R, Pellock SJ, Lauko A, Lee GR, An L, Dauparas J, DiMaio F, Baker D. Modeling protein-small molecule conformational ensembles with ChemNet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.25.614868. [PMID: 39386615 PMCID: PMC11463446 DOI: 10.1101/2024.09.25.614868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
17
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]
18
McGuffin LJ, Alharbi SMA. ModFOLD9: A Web Server for Independent Estimates of 3D Protein Model Quality. J Mol Biol 2024;436:168531. [PMID: 39237204 DOI: 10.1016/j.jmb.2024.168531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 09/07/2024]
19
Kovalevskiy O, Mateos-Garcia J, Tunyasuvunakool K. AlphaFold two years on: Validation and impact. Proc Natl Acad Sci U S A 2024;121:e2315002121. [PMID: 39133843 PMCID: PMC11348012 DOI: 10.1073/pnas.2315002121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]  Open
20
Kumar H, Kim P. Artificial intelligence in fusion protein three-dimensional structure prediction: Review and perspective. Clin Transl Med 2024;14:e1789. [PMID: 39090739 PMCID: PMC11294035 DOI: 10.1002/ctm2.1789] [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: 03/22/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]  Open
21
Chen L, Li Q, Nasif KFA, Xie Y, Deng B, Niu S, Pouriyeh S, Dai Z, Chen J, Xie CY. AI-Driven Deep Learning Techniques in Protein Structure Prediction. Int J Mol Sci 2024;25:8426. [PMID: 39125995 PMCID: PMC11313475 DOI: 10.3390/ijms25158426] [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: 07/15/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]  Open
22
Chen L, Mondal A, Perez A, Miranda-Quintana RA. Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices. J Chem Theory Comput 2024;20:6303-6315. [PMID: 38978294 PMCID: PMC11807272 DOI: 10.1021/acs.jctc.4c00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
23
Wang X, Guillem-Marti J, Kumar S, Lee DS, Cabrerizo-Aguado D, Werther R, Alamo KAE, Zhao YT, Nguyen A, Kopyeva I, Huang B, Li J, Hao Y, Li X, Brizuela-Velasco A, Murray A, Gerben S, Roy A, DeForest CA, Springer T, Ruohola-Baker H, Cooper JA, Campbell MG, Manero JM, Ginebra MP, Baker D. De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600123. [PMID: 38979380 PMCID: PMC11230231 DOI: 10.1101/2024.06.21.600123] [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]
24
Cervantes PW, Segelke BW, Lau EY, Robinson BV, Abisoye-Ogunniyan A, Pal S, de la Maza LM, Coleman MA, D’haeseleer P. Sequence, structure prediction, and epitope analysis of the polymorphic membrane protein family in Chlamydia trachomatis. PLoS One 2024;19:e0304525. [PMID: 38861498 PMCID: PMC11166332 DOI: 10.1371/journal.pone.0304525] [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: 11/01/2023] [Accepted: 05/13/2024] [Indexed: 06/13/2024]  Open
25
Han Y, Lu Y, Yan X, Cui H, Cheng S, Zheng J, Zhou Y, Wang S, Li Z. Atom-ProteinQA: Atom-level protein model quality assessment through fine-grained joint learning. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024;249:108078. [PMID: 38537495 DOI: 10.1016/j.cmpb.2024.108078] [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: 08/08/2023] [Revised: 12/26/2023] [Accepted: 02/10/2024] [Indexed: 04/21/2024]
26
Yang W, Hicks DR, Ghosh A, Schwartze TA, Conventry B, Goreshnik I, Allen A, Halabiya SF, Kim CJ, Hinck CS, Lee DS, Bera AK, Li Z, Wang Y, Schlichthaerle T, Cao L, Huang B, Garrett S, Gerben SR, Rettie S, Heine P, Murray A, Edman N, Carter L, Stewart L, Almo S, Hinck AP, Baker D. Design of High Affinity Binders to Convex Protein Target Sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592114. [PMID: 38746206 PMCID: PMC11092582 DOI: 10.1101/2024.05.01.592114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
27
Moon J, Hu G, Hayashi T. Application of Machine Learning in the Quantitative Analysis of the Surface Characteristics of Highly Abundant Cytoplasmic Proteins: Toward AI-Based Biomimetics. Biomimetics (Basel) 2024;9:162. [PMID: 38534847 DOI: 10.3390/biomimetics9030162] [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: 12/14/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]  Open
28
Morehead A, Liu J, Cheng J. Protein structure accuracy estimation using geometry-complete perceptron networks. Protein Sci 2024;33:e4932. [PMID: 38380738 PMCID: PMC10880424 DOI: 10.1002/pro.4932] [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: 07/22/2023] [Revised: 01/05/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024]
29
Li G, Yao S, Fan L. ProSTAGE: Predicting Effects of Mutations on Protein Stability by Using Protein Embeddings and Graph Convolutional Networks. J Chem Inf Model 2024;64:340-347. [PMID: 38166383 PMCID: PMC10806799 DOI: 10.1021/acs.jcim.3c01697] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024]
30
Zheng L, Shi S, Sun X, Lu M, Liao Y, Zhu S, Zhang H, Pan Z, Fang P, Zeng Z, Li H, Li Z, Xue W, Zhu F. MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Brief Bioinform 2024;25:bbae006. [PMID: 38305456 PMCID: PMC10835750 DOI: 10.1093/bib/bbae006] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 02/03/2024]  Open
31
Studer G, Tauriello G, Schwede T. Assessment of the assessment-All about complexes. Proteins 2023;91:1850-1860. [PMID: 37858934 DOI: 10.1002/prot.26612] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
32
Boohar RT, Vandepas LE, Traylor-Knowles N, Browne WE. Phylogenetic and Protein Structure Analyses Provide Insight into the Evolution and Diversification of the CD36 Domain "Apex" among Scavenger Receptor Class B Proteins across Eukarya. Genome Biol Evol 2023;15:evad218. [PMID: 38035778 PMCID: PMC10715195 DOI: 10.1093/gbe/evad218] [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: 12/27/2022] [Revised: 11/07/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]  Open
33
Debroy B, Chowdhury S, Pal K. Designing a novel and combinatorial multi-antigenic epitope-based vaccine "MarVax" against Marburg virus-a reverse vaccinology and immunoinformatics approach. J Genet Eng Biotechnol 2023;21:143. [PMID: 38012426 PMCID: PMC10681968 DOI: 10.1186/s43141-023-00575-w] [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: 05/20/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023]
34
Roy S, Ben-Hur A. Protein quality assessment with a loss function designed for high-quality decoys. FRONTIERS IN BIOINFORMATICS 2023;3:1198218. [PMID: 37915563 PMCID: PMC10616882 DOI: 10.3389/fbinf.2023.1198218] [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: 03/31/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]  Open
35
Liu J, Liu D, Zhang GJ. DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes. Bioinformatics 2023;39:btad591. [PMID: 37740296 PMCID: PMC10560100 DOI: 10.1093/bioinformatics/btad591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023]  Open
36
Li L, Zhou L, Jiang C, Liu Z, Meng D, Luo F, He Q, Yin H. AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia. Front Microbiol 2023;14:1243987. [PMID: 37744906 PMCID: PMC10512742 DOI: 10.3389/fmicb.2023.1243987] [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: 06/21/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]  Open
37
Tang HS, Gates CR, Schultz MC. Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus. PLoS One 2023;18:e0290892. [PMID: 37651389 PMCID: PMC10470895 DOI: 10.1371/journal.pone.0290892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]  Open
38
Jowsey W, Morris CP, Hall D, Sullivan J, Fagerlund R, Eto K, Solomon P, Mackay J, Bond C, Ramsay J, Ronson C. DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria. Nucleic Acids Res 2023;51:6841-6856. [PMID: 37246713 PMCID: PMC10359603 DOI: 10.1093/nar/gkad457] [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: 02/16/2023] [Revised: 05/04/2023] [Accepted: 05/12/2023] [Indexed: 05/30/2023]  Open
39
Reggiano G, Lugmayr W, Farrell D, Marlovits TC, DiMaio F. Residue-level error detection in cryoelectron microscopy models. Structure 2023;31:860-869.e4. [PMID: 37253357 PMCID: PMC10330749 DOI: 10.1016/j.str.2023.05.002] [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: 01/11/2023] [Revised: 02/16/2023] [Accepted: 05/03/2023] [Indexed: 06/01/2023]
40
He C, Ye X, Yang Y, Hu L, Si Y, Zhao X, Chen L, Fang Q, Wei Y, Wu F, Ye G. DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins. Brief Bioinform 2023:bbad246. [PMID: 37385595 DOI: 10.1093/bib/bbad246] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/08/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]  Open
41
Camponeschi C, Righino B, Pirolli D, Semeraro A, Ria F, De Rosa MC. Prediction of CD44 Structure by Deep Learning-Based Protein Modeling. Biomolecules 2023;13:1047. [PMID: 37509083 PMCID: PMC10376988 DOI: 10.3390/biom13071047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/19/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023]  Open
42
He G, Liu J, Liu D, Zhang G. GraphGPSM: a global scoring model for protein structure using graph neural networks. Brief Bioinform 2023:bbad219. [PMID: 37317619 DOI: 10.1093/bib/bbad219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/14/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]  Open
43
Mezősi-Csaplár M, Szöőr Á, Vereb G. CD28 and 41BB Costimulatory Domains Alone or in Combination Differentially Influence Cell Surface Dynamics and Organization of Chimeric Antigen Receptors and Early Activation of CAR T Cells. Cancers (Basel) 2023;15:3081. [PMID: 37370693 DOI: 10.3390/cancers15123081] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]  Open
44
Bennett NR, Coventry B, Goreshnik I, Huang B, Allen A, Vafeados D, Peng YP, Dauparas J, Baek M, Stewart L, DiMaio F, De Munck S, Savvides SN, Baker D. Improving de novo protein binder design with deep learning. Nat Commun 2023;14:2625. [PMID: 37149653 PMCID: PMC10163288 DOI: 10.1038/s41467-023-38328-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/24/2023] [Indexed: 05/08/2023]  Open
45
Wu T, Guo Z, Cheng J. Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. Bioinformatics 2023;39:btad298. [PMID: 37144951 PMCID: PMC10191610 DOI: 10.1093/bioinformatics/btad298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/18/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]  Open
46
Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023;64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
47
Liu J, Yuan R, Shao W, Wang J, Silman I, Sussman JL. Do "Newly Born" orphan proteins resemble "Never Born" proteins? A study using three deep learning algorithms. Proteins 2023. [PMID: 37092778 DOI: 10.1002/prot.26496] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/26/2023] [Accepted: 04/01/2023] [Indexed: 04/25/2023]
48
Gutnik D, Evseev P, Miroshnikov K, Shneider M. Using AlphaFold Predictions in Viral Research. Curr Issues Mol Biol 2023;45:3705-3732. [PMID: 37185764 PMCID: PMC10136805 DOI: 10.3390/cimb45040240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]  Open
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Dichio V, Zeng HL, Aurell E. Statistical genetics in and out of quasi-linkage equilibrium. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023;86:052601. [PMID: 36944245 DOI: 10.1088/1361-6633/acc5fa] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
50
Lankiewicz TS, Choudhary H, Gao Y, Amer B, Lillington SP, Leggieri PA, Brown JL, Swift CL, Lipzen A, Na H, Amirebrahimi M, Theodorou MK, Baidoo EEK, Barry K, Grigoriev IV, Timokhin VI, Gladden J, Singh S, Mortimer JC, Ralph J, Simmons BA, Singer SW, O'Malley MA. Lignin deconstruction by anaerobic fungi. Nat Microbiol 2023;8:596-610. [PMID: 36894634 PMCID: PMC10066034 DOI: 10.1038/s41564-023-01336-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023]
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