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For: Liu Y, Ye Q, Wang L, Peng J. Learning structural motif representations for efficient protein structure search. Bioinformatics 2019;34:i773-i780. [PMID: 30423083 PMCID: PMC6129266 DOI: 10.1093/bioinformatics/bty585] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Cheng P, Mao C, Tang J, Yang S, Cheng Y, Wang W, Gu Q, Han W, Chen H, Li S, Chen Y, Zhou J, Li W, Pan A, Zhao S, Huang X, Zhu S, Zhang J, Shu W, Wang S. Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering. Cell Res 2024:10.1038/s41422-024-00989-2. [PMID: 38969803 DOI: 10.1038/s41422-024-00989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024]  Open
2
Liu Z, Zhang C, Zhang Q, Zhang Y, Yu DJ. TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J Chem Inf Model 2024;64:1043-1049. [PMID: 38270339 DOI: 10.1021/acs.jcim.3c01455] [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: 01/26/2024]
3
Durairaj J, de Ridder D, van Dijk AD. Beyond sequence: Structure-based machine learning. Comput Struct Biotechnol J 2022;21:630-643. [PMID: 36659927 PMCID: PMC9826903 DOI: 10.1016/j.csbj.2022.12.039] [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: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]  Open
4
To Affinity and Beyond: A Personal Reflection on the Design and Discovery of Drugs. Molecules 2022;27:molecules27217624. [DOI: 10.3390/molecules27217624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022]  Open
5
Xia C, Feng SH, Xia Y, Pan X, Shen HB. Fast protein structure comparison through effective representation learning with contrastive graph neural networks. PLoS Comput Biol 2022;18:e1009986. [PMID: 35324898 PMCID: PMC8982879 DOI: 10.1371/journal.pcbi.1009986] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/05/2022] [Accepted: 03/03/2022] [Indexed: 12/03/2022]  Open
6
Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022;14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022]  Open
7
Reza MS, Zhang H, Hossain MT, Jin L, Feng S, Wei Y. COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization. MEMBRANES 2021;11:membranes11070503. [PMID: 34209399 PMCID: PMC8305966 DOI: 10.3390/membranes11070503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
8
Bahai A, Asgari E, Mofrad MRK, Kloetgen A, McHardy AC. EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings. Bioinformatics 2021;37:4517-4525. [PMID: 34180989 PMCID: PMC8652027 DOI: 10.1093/bioinformatics/btab467] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/28/2021] [Accepted: 06/25/2021] [Indexed: 11/19/2022]  Open
9
Villegas-Morcillo A, Makrodimitris S, van Ham RCHJ, Gomez AM, Sanchez V, Reinders MJT. Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. Bioinformatics 2021;37:162-170. [PMID: 32797179 PMCID: PMC8055213 DOI: 10.1093/bioinformatics/btaa701] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/10/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022]  Open
10
Durairaj J, Akdel M, de Ridder D, van Dijk ADJ. Geometricus represents protein structures as shape-mers derived from moment invariants. Bioinformatics 2021;36:i718-i725. [PMID: 33381814 DOI: 10.1093/bioinformatics/btaa839] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 01/28/2023]  Open
11
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
12
Swanson K, Trivedi S, Lequieu J, Swanson K, Kondor R. Deep learning for automated classification and characterization of amorphous materials. SOFT MATTER 2020;16:435-446. [PMID: 31803878 DOI: 10.1039/c9sm01903k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
13
Su Y, Luo Y, Zhao X, Liu Y, Peng J. Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction. PLoS Comput Biol 2019;15:e1007283. [PMID: 31483777 PMCID: PMC6752863 DOI: 10.1371/journal.pcbi.1007283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/19/2019] [Accepted: 07/24/2019] [Indexed: 11/23/2022]  Open
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