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For: Karimi M, Zhu S, Cao Y, Shen Y. De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. J Chem Inf Model 2020;60:5667-5681. [PMID: 32945673 PMCID: PMC7775287 DOI: 10.1021/acs.jcim.0c00593] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Number Cited by Other Article(s)
1
Jiang J, Zhang C, Ke L, Hayes N, Zhu Y, Qiu H, Zhang B, Zhou T, Wei GW. A review of machine learning methods for imbalanced data challenges in chemistry. Chem Sci 2025;16:7637-7658. [PMID: 40271022 PMCID: PMC12013631 DOI: 10.1039/d5sc00270b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Accepted: 04/06/2025] [Indexed: 04/25/2025]  Open
2
Zhong J, Zou Z, Qiu J, Wang S. ScFold: a GNN-based model for efficient inverse folding of short-chain proteins via spatial reduction. Brief Bioinform 2025;26:bbaf156. [PMID: 40205854 PMCID: PMC11982017 DOI: 10.1093/bib/bbaf156] [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: 11/04/2024] [Revised: 02/24/2025] [Accepted: 03/19/2025] [Indexed: 04/11/2025]  Open
3
Guan C, Fernandes FC, Franco OL, de la Fuente-Nunez C. Leveraging large language models for peptide antibiotic design. CELL REPORTS. PHYSICAL SCIENCE 2025;6:102359. [PMID: 39949833 PMCID: PMC11823563 DOI: 10.1016/j.xcrp.2024.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2025]
4
Wang Z, Yuan H, Yan J, Liu J. Identification, characterization, and design of plant genome sequences using deep learning. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025;121:e17190. [PMID: 39666835 DOI: 10.1111/tpj.17190] [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: 09/03/2024] [Revised: 11/11/2024] [Accepted: 11/23/2024] [Indexed: 12/14/2024]
5
Li S, Peng L, Chen L, Que L, Kang W, Hu X, Ma J, Di Z, Liu Y. Discovery of Highly Bioactive Peptides through Hierarchical Structural Information and Molecular Dynamics Simulations. J Chem Inf Model 2024;64:8164-8175. [PMID: 39466714 DOI: 10.1021/acs.jcim.4c01006] [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: 10/30/2024]
6
Satalkar V, Degaga GD, Li W, Pang YT, McShan AC, Gumbart JC, Mitchell JC, Torres MP. Generative β-hairpin design using a residue-based physicochemical property landscape. Biophys J 2024;123:2790-2806. [PMID: 38297834 PMCID: PMC11393682 DOI: 10.1016/j.bpj.2024.01.029] [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: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/02/2024]  Open
7
Ding N, Yuan Z, Ma Z, Wu Y, Yin L. AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors. Molecules 2024;29:3512. [PMID: 39124917 PMCID: PMC11313831 DOI: 10.3390/molecules29153512] [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: 06/27/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]  Open
8
Wang H, Liu D, Zhao K, Wang Y, Zhang G. SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition. Brief Bioinform 2024;25:bbae146. [PMID: 38600663 PMCID: PMC11006797 DOI: 10.1093/bib/bbae146] [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: 01/01/2024] [Revised: 03/02/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]  Open
9
Hu X, Lin C, Chen T, Chen W. Interactive design generation and optimization from generative adversarial networks in spatial computing. Sci Rep 2024;14:5154. [PMID: 38431717 PMCID: PMC10908823 DOI: 10.1038/s41598-024-54783-6] [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: 10/09/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]  Open
10
Guo Z, Liu J, Wang Y, Chen M, Wang D, Xu D, Cheng J. Diffusion models in bioinformatics and computational biology. NATURE REVIEWS BIOENGINEERING 2024;2:136-154. [PMID: 38576453 PMCID: PMC10994218 DOI: 10.1038/s44222-023-00114-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 04/06/2024]
11
Michalik I, Kuder KJ. Machine Learning Methods in Protein-Protein Docking. Methods Mol Biol 2024;2780:107-126. [PMID: 38987466 DOI: 10.1007/978-1-0716-3985-6_7] [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] [Indexed: 07/12/2024]
12
Barghout RA, Xu Z, Betala S, Mahadevan R. Advances in generative modeling methods and datasets to design novel enzymes for renewable chemicals and fuels. Curr Opin Biotechnol 2023;84:103007. [PMID: 37931573 DOI: 10.1016/j.copbio.2023.103007] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023]
13
Mallik BB, Stanislaw J, Alawathurage TM, Khmelinskaia A. De Novo Design of Polyhedral Protein Assemblies: Before and After the AI Revolution. Chembiochem 2023;24:e202300117. [PMID: 37014094 DOI: 10.1002/cbic.202300117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023]
14
Xie X, Valiente PA, Kim PM. HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. Bioinformatics 2023;39:6991169. [PMID: 36651657 PMCID: PMC9887083 DOI: 10.1093/bioinformatics/btad036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023]  Open
15
Liu J, Zhang C, Lai L. GeoPacker: A novel deep learning framework for protein side-chain modeling. Protein Sci 2022;31:e4484. [PMID: 36309961 PMCID: PMC9667900 DOI: 10.1002/pro.4484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
16
Ramos EK, Tsai CF, Jia Y, Cao Y, Manu M, Taftaf R, Hoffmann AD, El-Shennawy L, Gritsenko MA, Adorno-Cruz V, Schuster EJ, Scholten D, Patel D, Liu X, Patel P, Wray B, Zhang Y, Zhang S, Moore RJ, Mathews JV, Schipma MJ, Liu T, Tokars VL, Cristofanilli M, Shi T, Shen Y, Dashzeveg NK, Liu H. Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. eLife 2022;11:e82669. [PMID: 36193887 PMCID: PMC9581534 DOI: 10.7554/elife.82669] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]  Open
17
Zatorski N, Stein D, Rahman R, Iyengar R, Schlessinger A. Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. Database (Oxford) 2022;2022:6650186. [PMID: 35881481 PMCID: PMC9319604 DOI: 10.1093/database/baac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/05/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022]
18
Freschlin CR, Fahlberg SA, Romero PA. Machine learning to navigate fitness landscapes for protein engineering. Curr Opin Biotechnol 2022;75:102713. [PMID: 35413604 PMCID: PMC9177649 DOI: 10.1016/j.copbio.2022.102713] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/05/2022] [Accepted: 02/28/2022] [Indexed: 11/19/2022]
19
Ding W, Nakai K, Gong H. Protein design via deep learning. Brief Bioinform 2022;23:bbac102. [PMID: 35348602 PMCID: PMC9116377 DOI: 10.1093/bib/bbac102] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/26/2022] [Accepted: 03/01/2022] [Indexed: 12/11/2022]  Open
20
Talluri S. Algorithms for protein design. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022;130:1-38. [PMID: 35534105 DOI: 10.1016/bs.apcsb.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
21
Lin E, Lin CH, Lane HY. De Novo Peptide and Protein Design Using Generative Adversarial Networks: An Update. J Chem Inf Model 2022;62:761-774. [DOI: 10.1021/acs.jcim.1c01361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Deep generative modeling for protein design. Curr Opin Struct Biol 2021;72:226-236. [PMID: 34963082 DOI: 10.1016/j.sbi.2021.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/01/2021] [Accepted: 11/22/2021] [Indexed: 11/21/2022]
23
De novo protein design by deep network hallucination. Nature 2021;600:547-552. [PMID: 34853475 DOI: 10.1038/s41586-021-04184-w] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/21/2021] [Indexed: 12/25/2022]
24
Defresne M, Barbe S, Schiex T. Protein Design with Deep Learning. Int J Mol Sci 2021;22:11741. [PMID: 34769173 PMCID: PMC8584038 DOI: 10.3390/ijms222111741] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/26/2021] [Indexed: 12/21/2022]  Open
25
Kosugi T, Ohue M. Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions. Int J Mol Sci 2021;22:10925. [PMID: 34681589 PMCID: PMC8539639 DOI: 10.3390/ijms222010925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]  Open
26
Sacha M, Błaż M, Byrski P, Dąbrowski-Tumański P, Chromiński M, Loska R, Włodarczyk-Pruszyński P, Jastrzębski S. Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits. J Chem Inf Model 2021;61:3273-3284. [PMID: 34251814 DOI: 10.1021/acs.jcim.1c00537] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
27
Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. PROCEEDINGS OF MACHINE LEARNING RESEARCH 2021;139:1261-1271. [PMID: 34423306 PMCID: PMC8375603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
28
Tripathi MK, Nath A, Singh TP, Ethayathulla AS, Kaur P. Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. Mol Divers 2021;25:1439-1460. [PMID: 34159484 PMCID: PMC8219515 DOI: 10.1007/s11030-021-10256-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022]
29
Osadchy M, Kolodny R. How Deep Learning Tools Can Help Protein Engineers Find Good Sequences. J Phys Chem B 2021;125:6440-6450. [PMID: 34105961 DOI: 10.1021/acs.jpcb.1c02449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
30
Narayanan H, Dingfelder F, Butté A, Lorenzen N, Sokolov M, Arosio P. Machine Learning for Biologics: Opportunities for Protein Engineering, Developability, and Formulation. Trends Pharmacol Sci 2021;42:151-165. [DOI: 10.1016/j.tips.2020.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/10/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
31
Pan X, Kortemme T. Recent advances in de novo protein design: Principles, methods, and applications. J Biol Chem 2021;296:100558. [PMID: 33744284 PMCID: PMC8065224 DOI: 10.1016/j.jbc.2021.100558] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]  Open
32
Merz KM, De Fabritiis G, Wei GW. Generative Models for Molecular Design. J Chem Inf Model 2020;60:5635-5636. [PMID: 33378853 DOI: 10.1021/acs.jcim.0c01388] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
33
Gao W, Mahajan SP, Sulam J, Gray JJ. Deep Learning in Protein Structural Modeling and Design. PATTERNS (NEW YORK, N.Y.) 2020;1:100142. [PMID: 33336200 PMCID: PMC7733882 DOI: 10.1016/j.patter.2020.100142] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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