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For: Torng W, Altman RB. 3D deep convolutional neural networks for amino acid environment similarity analysis. BMC Bioinformatics 2017;18:302. [PMID: 28615003 PMCID: PMC5472009 DOI: 10.1186/s12859-017-1702-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023]  Open
Number Cited by Other Article(s)
1
Li B, Luo S, Wang W, Xu J, Liu D, Shameem M, Mattila J, Franklin MC, Hawkins PG, Atwal GS. PROPERMAB: an integrative framework for in silico prediction of antibody developability using machine learning. MAbs 2025;17:2474521. [PMID: 40042626 PMCID: PMC11901398 DOI: 10.1080/19420862.2025.2474521] [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: 11/05/2024] [Revised: 02/25/2025] [Accepted: 02/26/2025] [Indexed: 03/14/2025]  Open
2
Bjerregaard A, Groth PM, Hauberg S, Krogh A, Boomsma W. Foundation models of protein sequences: A brief overview. Curr Opin Struct Biol 2025;91:103004. [PMID: 39983412 DOI: 10.1016/j.sbi.2025.103004] [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: 09/16/2024] [Revised: 01/24/2025] [Accepted: 01/26/2025] [Indexed: 02/23/2025]
3
Allman BE, Vieira L, Diaz DJ, Wilke CO. A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks. J R Soc Interface 2025;22:20240598. [PMID: 40300635 PMCID: PMC12040448 DOI: 10.1098/rsif.2024.0598] [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: 08/29/2024] [Revised: 01/02/2025] [Accepted: 02/18/2025] [Indexed: 05/01/2025]  Open
4
Powers AC, Renfrew PD, Hosseinzadeh P, Mulligan VK. CYCLICCAE: A CONFORMATIONAL AUTOENCODER FOR EFFICIENT HETEROCHIRAL MACROCYCLIC BACKBONE SAMPLING. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.21.639569. [PMID: 40060652 PMCID: PMC11888347 DOI: 10.1101/2025.02.21.639569] [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]
5
Ertelt M, Moretti R, Meiler J, Schoeder CT. Self-supervised machine learning methods for protein design improve sampling but not the identification of high-fitness variants. SCIENCE ADVANCES 2025;11:eadr7338. [PMID: 39937901 PMCID: PMC11817935 DOI: 10.1126/sciadv.adr7338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 01/10/2025] [Indexed: 02/14/2025]
6
Harding-Larsen D, Funk J, Madsen NG, Gharabli H, Acevedo-Rocha CG, Mazurenko S, Welner DH. Protein representations: Encoding biological information for machine learning in biocatalysis. Biotechnol Adv 2024;77:108459. [PMID: 39366493 DOI: 10.1016/j.biotechadv.2024.108459] [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: 04/18/2024] [Revised: 09/19/2024] [Accepted: 09/29/2024] [Indexed: 10/06/2024]
7
Bakkers MJG, Ritschel T, Tiemessen M, Dijkman J, Zuffianò AA, Yu X, van Overveld D, Le L, Voorzaat R, van Haaren MM, de Man M, Tamara S, van der Fits L, Zahn R, Juraszek J, Langedijk JPM. Efficacious human metapneumovirus vaccine based on AI-guided engineering of a closed prefusion trimer. Nat Commun 2024;15:6270. [PMID: 39054318 PMCID: PMC11272930 DOI: 10.1038/s41467-024-50659-5] [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: 02/20/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]  Open
8
Branda F, Scarpa F. Implications of Artificial Intelligence in Addressing Antimicrobial Resistance: Innovations, Global Challenges, and Healthcare's Future. Antibiotics (Basel) 2024;13:502. [PMID: 38927169 PMCID: PMC11200959 DOI: 10.3390/antibiotics13060502] [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: 04/30/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]  Open
9
Goshisht MK. Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges. ACS OMEGA 2024;9:9921-9945. [PMID: 38463314 PMCID: PMC10918679 DOI: 10.1021/acsomega.3c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
10
Parrilla-Gutiérrez JM, Granda JM, Ayme JF, Bajczyk MD, Wilbraham L, Cronin L. Electron density-based GPT for optimization and suggestion of host-guest binders. NATURE COMPUTATIONAL SCIENCE 2024;4:200-209. [PMID: 38459272 DOI: 10.1038/s43588-024-00602-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/23/2024] [Indexed: 03/10/2024]
11
Pun MN, Ivanov A, Bellamy Q, Montague Z, LaMont C, Bradley P, Otwinowski J, Nourmohammad A. Learning the shape of protein microenvironments with a holographic convolutional neural network. Proc Natl Acad Sci U S A 2024;121:e2300838121. [PMID: 38300863 PMCID: PMC10861886 DOI: 10.1073/pnas.2300838121] [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: 01/18/2023] [Accepted: 11/29/2023] [Indexed: 02/03/2024]  Open
12
Liu Y, Liu H. Protein sequence design on given backbones with deep learning. Protein Eng Des Sel 2024;37:gzad024. [PMID: 38157313 DOI: 10.1093/protein/gzad024] [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: 08/16/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]  Open
13
Chowdhury J, Fricke C, Bamidele O, Bello M, Yang W, Heyden A, Terejanu G. Invariant Molecular Representations for Heterogeneous Catalysis. J Chem Inf Model 2024;64:327-339. [PMID: 38197612 PMCID: PMC10806804 DOI: 10.1021/acs.jcim.3c00594] [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: 07/26/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/11/2024]
14
Ugurlu SY, McDonald D, Lei H, Jones AM, Li S, Tong HY, Butler MS, He S. Cobdock: an accurate and practical machine learning-based consensus blind docking method. J Cheminform 2024;16:5. [PMID: 38212855 PMCID: PMC10785400 DOI: 10.1186/s13321-023-00793-x] [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: 03/27/2023] [Accepted: 12/10/2023] [Indexed: 01/13/2024]  Open
15
Rahman H, Khan AR, Sadiq T, Farooqi AH, Khan IU, Lim WH. A Systematic Literature Review of 3D Deep Learning Techniques in Computed Tomography Reconstruction. Tomography 2023;9:2158-2189. [PMID: 38133073 PMCID: PMC10748093 DOI: 10.3390/tomography9060169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]  Open
16
Yue T, Wang Y, Zhang L, Gu C, Xue H, Wang W, Lyu Q, Dun Y. Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models. Int J Mol Sci 2023;24:15858. [PMID: 37958843 PMCID: PMC10649223 DOI: 10.3390/ijms242115858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]  Open
17
Xiao B, Zhang C, Zhou J, Wang S, Meng H, Wu M, Zheng Y, Yu R. Design of SC PEP with enhanced stability against pepsin digestion and increased activity by machine learning and structural parameters modeling. Int J Biol Macromol 2023;250:125933. [PMID: 37482154 DOI: 10.1016/j.ijbiomac.2023.125933] [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: 01/09/2023] [Revised: 06/20/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
18
Guo L, Qiu T, Wang J. ViTScore: A Novel Three-Dimensional Vision Transformer Method for Accurate Prediction of Protein-Ligand Docking Poses. IEEE Trans Nanobioscience 2023;22:734-743. [PMID: 37159314 DOI: 10.1109/tnb.2023.3274640] [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: 05/11/2023]
19
Sieg J, Rarey M. Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Brief Bioinform 2023;24:bbad357. [PMID: 37833838 DOI: 10.1093/bib/bbad357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]  Open
20
Sinha K, Ghosh N, Sil PC. A Review on the Recent Applications of Deep Learning in Predictive Drug Toxicological Studies. Chem Res Toxicol 2023;36:1174-1205. [PMID: 37561655 DOI: 10.1021/acs.chemrestox.2c00375] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
21
Kulikova AV, Diaz DJ, Chen T, Cole TJ, Ellington AD, Wilke CO. Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry. Sci Rep 2023;13:13280. [PMID: 37587128 PMCID: PMC10432456 DOI: 10.1038/s41598-023-40247-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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/18/2023]  Open
22
Niazi SK, Mariam Z. Recent Advances in Machine-Learning-Based Chemoinformatics: A Comprehensive Review. Int J Mol Sci 2023;24:11488. [PMID: 37511247 PMCID: PMC10380192 DOI: 10.3390/ijms241411488] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]  Open
23
Kulikova AV, Diaz DJ, Chen T, Jeffrey Cole T, Ellington AD, Wilke CO. Two sequence- and two structure-based ML models have learned different aspects of protein biochemistry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533508. [PMID: 36993648 PMCID: PMC10055221 DOI: 10.1101/2023.03.20.533508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
24
Ramakrishnan G, Baakman C, Heijl S, Vroling B, van Horck R, Hiraki J, Xue LC, Huynen MA. Understanding structure-guided variant effect predictions using 3D convolutional neural networks. Front Mol Biosci 2023;10:1204157. [PMID: 37475887 PMCID: PMC10354367 DOI: 10.3389/fmolb.2023.1204157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023]  Open
25
Dürr SL, Levy A, Rothlisberger U. Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins. Nat Commun 2023;14:2713. [PMID: 37169763 PMCID: PMC10175565 DOI: 10.1038/s41467-023-37870-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/29/2023] [Indexed: 05/13/2023]  Open
26
Xu G, Wang Q, Ma J. OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling. J Chem Theory Comput 2023;19:1629-1640. [PMID: 36813264 PMCID: PMC10018731 DOI: 10.1021/acs.jctc.2c00847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
27
Rappoport D, Jinich A. Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves. J Chem Inf Model 2023;63:1637-1648. [PMID: 36802628 DOI: 10.1021/acs.jcim.3c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
28
Meller A, Ward M, Borowsky J, Kshirsagar M, Lotthammer JM, Oviedo F, Ferres JL, Bowman GR. Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network. Nat Commun 2023;14:1177. [PMID: 36859488 PMCID: PMC9977097 DOI: 10.1038/s41467-023-36699-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023]  Open
29
Oostrom M, Akers S, Garrett N, Hanson E, Shaw W, Laureanti JA. Classifying metal-binding sites with neural networks. Protein Sci 2023;32:e4591. [PMID: 36775934 PMCID: PMC9951193 DOI: 10.1002/pro.4591] [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: 09/12/2022] [Revised: 01/30/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023]
30
Diaz DJ, Kulikova AV, Ellington AD, Wilke CO. Using machine learning to predict the effects and consequences of mutations in proteins. Curr Opin Struct Biol 2023;78:102518. [PMID: 36603229 PMCID: PMC9908841 DOI: 10.1016/j.sbi.2022.102518] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/07/2022] [Accepted: 11/20/2022] [Indexed: 01/05/2023]
31
Zhang S, Yang K, Liu Z, Lai X, Yang Z, Zeng J, Li S. DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms. Brief Bioinform 2023;24:6918762. [PMID: 36527428 DOI: 10.1093/bib/bbac526] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/17/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022]  Open
32
Paik I, Ngo PHT, Shroff R, Diaz DJ, Maranhao AC, Walker DJ, Bhadra S, Ellington AD. Improved Bst DNA Polymerase Variants Derived via a Machine Learning Approach. Biochemistry 2023;62:410-418. [PMID: 34762799 PMCID: PMC9514386 DOI: 10.1021/acs.biochem.1c00451] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
33
Kosonocky CW, Ellington AD. Evolving to Evolve, Dan Tawfik's Insights into Protein Engineering. Biochemistry 2023;62:145-147. [PMID: 36647679 DOI: 10.1021/acs.biochem.2c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
34
Gupta S, Baudry J, Menon V. Big Data analytics for improved prediction of ligand binding and conformational selection. Front Mol Biosci 2023;9:953984. [PMID: 36710883 PMCID: PMC9878559 DOI: 10.3389/fmolb.2022.953984] [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: 05/26/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]  Open
35
Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023;2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
36
Molecular Dynamics Simulation of Poly(Ether Ether Ketone) (PEEK) Polymer to Analyze Intermolecular Ordering by Low Wavenumber Raman Spectroscopy and X-ray Diffraction. Polymers (Basel) 2022;14:polym14245406. [PMID: 36559773 PMCID: PMC9786246 DOI: 10.3390/polym14245406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]  Open
37
Liu H, Chen Q. Computational protein design with data‐driven approaches: Recent developments and perspectives. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
38
Zhao Y, Shao J, Asmann YW. Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022;20:899-911. [PMID: 35931322 PMCID: PMC10025763 DOI: 10.1016/j.gpb.2022.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/05/2022] [Accepted: 07/25/2022] [Indexed: 01/12/2023]
39
Wilman W, Wróbel S, Bielska W, Deszynski P, Dudzic P, Jaszczyszyn I, Kaniewski J, Młokosiewicz J, Rouyan A, Satława T, Kumar S, Greiff V, Krawczyk K. Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery. Brief Bioinform 2022;23:bbac267. [PMID: 35830864 PMCID: PMC9294429 DOI: 10.1093/bib/bbac267] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022]  Open
40
Liu Y, Zhang L, Wang W, Zhu M, Wang C, Li F, Zhang J, Li H, Chen Q, Liu H. Rotamer-free protein sequence design based on deep learning and self-consistency. NATURE COMPUTATIONAL SCIENCE 2022;2:451-462. [PMID: 38177863 DOI: 10.1038/s43588-022-00273-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 06/07/2022] [Indexed: 01/06/2024]
41
Misiura M, Shroff R, Thyer R, Kolomeisky AB. DLPacker: Deep learning for prediction of amino acid side chain conformations in proteins. Proteins 2022;90:1278-1290. [PMID: 35122328 DOI: 10.1002/prot.26311] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/20/2022]
42
Horne J, Shukla D. Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering. Ind Eng Chem Res 2022;61:6235-6245. [PMID: 36051311 PMCID: PMC9432854 DOI: 10.1021/acs.iecr.1c04943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Gupta AK, Raghavachari K. Three-Dimensional Convolutional Neural Networks Utilizing Molecular Topological Features for Accurate Atomization Energy Predictions. J Chem Theory Comput 2022;18:2132-2143. [PMID: 35226496 DOI: 10.1021/acs.jctc.1c00504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Guo L, He J, Lin P, Huang SY, Wang J. TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics 2022;38:2444-2451. [PMID: 35199137 DOI: 10.1093/bioinformatics/btac120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022]  Open
45
Anand N, Eguchi R, Mathews II, Perez CP, Derry A, Altman RB, Huang PS. Protein sequence design with a learned potential. Nat Commun 2022;13:746. [PMID: 35136054 PMCID: PMC8826426 DOI: 10.1038/s41467-022-28313-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/08/2022] [Indexed: 11/08/2022]  Open
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Ovchinnikov S, Huang PS. Structure-based protein design with deep learning. Curr Opin Chem Biol 2021;65:136-144. [PMID: 34547592 PMCID: PMC8671290 DOI: 10.1016/j.cbpa.2021.08.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022]
47
Tong X, Liu S, Gu J, Wu C, Liang Y, Shi X. Amino acid environment affinity model based on graph attention network. J Bioinform Comput Biol 2021;20:2150032. [PMID: 34775920 DOI: 10.1142/s0219720021500323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Learning the local landscape of protein structures with convolutional neural networks. J Biol Phys 2021;47:435-454. [PMID: 34751854 DOI: 10.1007/s10867-021-09593-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]  Open
49
Wang G, Zhai YJ, Xue ZZ, Xu YY. Improving Protein Subcellular Location Classification by Incorporating Three-Dimensional Structure Information. Biomolecules 2021;11:1607. [PMID: 34827605 PMCID: PMC8615982 DOI: 10.3390/biom11111607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022]  Open
50
Yu Y, Xu T, Li J, Qiu Y, Rong Y, Gong Z, Cheng X, Dong L, Liu W, Li J, Dou D, Huang J. A Novel Scalarized Scaffold Hopping Algorithm with Graph-Based Variational Autoencoder for Discovery of JAK1 Inhibitors. ACS OMEGA 2021;6:22945-22954. [PMID: 34514265 PMCID: PMC8427782 DOI: 10.1021/acsomega.1c03613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
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