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For: Seemayer S, Gruber M, Söding J. CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations. ACTA ACUST UNITED AC 2014;30:3128-30. [PMID: 25064567 PMCID: PMC4201158 DOI: 10.1093/bioinformatics/btu500] [Citation(s) in RCA: 281] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Number Cited by Other Article(s)
1
Yuan R, Zhang J, Zhou J, Cong Q. Recent progress and future challenges in structure-based protein-protein interaction prediction. Mol Ther 2025;33:2252-2268. [PMID: 40195117 DOI: 10.1016/j.ymthe.2025.04.003] [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: 02/07/2025] [Revised: 03/05/2025] [Accepted: 04/02/2025] [Indexed: 04/09/2025]  Open
2
Kumar SP, Nadendla EK, Malireddi RKS, Haque SA, Mall R, Neuwald AF, Kanneganti TD. Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis. Mol Biol Evol 2025;42:msaf096. [PMID: 40277230 PMCID: PMC12066828 DOI: 10.1093/molbev/msaf096] [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: 12/09/2024] [Revised: 04/09/2025] [Accepted: 04/15/2025] [Indexed: 04/26/2025]  Open
3
Almalki B, Liao L. Transmembrane Homodimers Interface Identification: Predicting Interface Residues in Alpha-Helical Transmembrane Protein Homodimers Using Sequential and Structural Features. Int J Mol Sci 2025;26:4270. [PMID: 40362505 PMCID: PMC12073085 DOI: 10.3390/ijms26094270] [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: 02/27/2025] [Revised: 04/11/2025] [Accepted: 04/17/2025] [Indexed: 05/15/2025]  Open
4
Xu M, Dantu SC, Garnett JA, Bonomo RA, Pandini A, Haider S. Functionally important residues from graph analysis of coevolved dynamic couplings. eLife 2025;14:RP105005. [PMID: 40153310 PMCID: PMC11952748 DOI: 10.7554/elife.105005] [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] [Indexed: 03/30/2025]  Open
5
Park S, Myung S, Baek M. Advancing protein structure prediction beyond AlphaFold2. Curr Opin Struct Biol 2025;90:102985. [PMID: 39862760 DOI: 10.1016/j.sbi.2025.102985] [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: 10/13/2024] [Revised: 12/31/2024] [Accepted: 01/02/2025] [Indexed: 01/27/2025]
6
Tikhonov DB, Korkosh VS, Zhorov BS. 3D-aligned tetrameric ion channels with universal residue labels for comparative structural analysis. Biophys J 2025;124:458-470. [PMID: 39696821 PMCID: PMC11788486 DOI: 10.1016/j.bpj.2024.12.019] [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: 05/21/2024] [Revised: 09/19/2024] [Accepted: 12/16/2024] [Indexed: 12/20/2024]  Open
7
Srivastava G, Liu M, Ni X, Pu L, Brylinski M. Machine Learning Techniques to Infer Protein Structure and Function from Sequences: A Comprehensive Review. Methods Mol Biol 2025;2867:79-104. [PMID: 39576576 DOI: 10.1007/978-1-0716-4196-5_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] [Indexed: 11/24/2024]
8
Qin X, Zhang L, Liu M, Liu G. PRFold-TNN: Protein Fold Recognition With an Ensemble Feature Selection Method Using PageRank Algorithm Based on Transformer. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1740-1751. [PMID: 38875077 DOI: 10.1109/tcbb.2024.3414497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
9
Zhang F, Li Z, Zhao K, Zhao P, Zhang G. Prediction of Inter-Residue Multiple Distances and Exploration of Protein Multiple Conformations by Deep Learning. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:1731-1739. [PMID: 38857126 DOI: 10.1109/tcbb.2024.3411825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
10
Heinzinger M, Rost B. Artificial Intelligence Learns Protein Prediction. Cold Spring Harb Perspect Biol 2024;16:a041458. [PMID: 38858069 PMCID: PMC11368192 DOI: 10.1101/cshperspect.a041458] [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: 06/12/2024]
11
Rahimzadeh F, Mohammad Khanli L, Salehpoor P, Golabi F, PourBahrami S. Unveiling the evolution of policies for enhancing protein structure predictions: A comprehensive analysis. Comput Biol Med 2024;179:108815. [PMID: 38986287 DOI: 10.1016/j.compbiomed.2024.108815] [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: 03/04/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
12
Illig AM, Siedhoff NE, Davari MD, Schwaneberg U. Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort. J Chem Inf Model 2024;64:6350-6360. [PMID: 39088689 DOI: 10.1021/acs.jcim.4c00704] [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: 08/03/2024]
13
Basu S, Subedi U, Tonelli M, Afshinpour M, Tiwari N, Fuentes EJ, Chakravarty S. Assessing the functional roles of coevolving PHD finger residues. Protein Sci 2024;33:e5065. [PMID: 38923615 PMCID: PMC11201814 DOI: 10.1002/pro.5065] [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: 10/31/2023] [Revised: 04/21/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024]
14
Jisna VA, Ajay AP, Jayaraj PB. Using Attention-UNet Models to Predict Protein Contact Maps. J Comput Biol 2024;31:691-702. [PMID: 38979621 DOI: 10.1089/cmb.2023.0102] [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: 07/10/2024]  Open
15
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct programmable recombination of target and donor DNA. Nature 2024;630:984-993. [PMID: 38926615 PMCID: PMC11208160 DOI: 10.1038/s41586-024-07552-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024]
16
Xie T, Huang J. Can Protein Structure Prediction Methods Capture Alternative Conformations of Membrane Transporters? J Chem Inf Model 2024;64:3524-3536. [PMID: 38564295 DOI: 10.1021/acs.jcim.3c01936] [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: 04/04/2024]
17
Si Y, Yan C. Protein language model-embedded geometric graphs power inter-protein contact prediction. eLife 2024;12:RP92184. [PMID: 38564241 PMCID: PMC10987090 DOI: 10.7554/elife.92184] [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] [Indexed: 04/04/2024]  Open
18
Zhang J, Durham J, Qian Cong. Revolutionizing protein-protein interaction prediction with deep learning. Curr Opin Struct Biol 2024;85:102775. [PMID: 38330793 DOI: 10.1016/j.sbi.2024.102775] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
19
Bibik P, Alibai S, Pandini A, Dantu SC. PyCoM: a python library for large-scale analysis of residue-residue coevolution data. Bioinformatics 2024;40:btae166. [PMID: 38532297 PMCID: PMC11009027 DOI: 10.1093/bioinformatics/btae166] [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: 09/19/2023] [Revised: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 03/28/2024]  Open
20
Qi H, Yu T, Yu W, Liu C. Drug-target affinity prediction with extended graph learning-convolutional networks. BMC Bioinformatics 2024;25:75. [PMID: 38365583 PMCID: PMC10874073 DOI: 10.1186/s12859-024-05698-6] [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: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]  Open
21
Zhao C, Wang S. AttCON: With better MSAs and attention mechanism for accurate protein contact map prediction. Comput Biol Med 2024;169:107822. [PMID: 38091726 DOI: 10.1016/j.compbiomed.2023.107822] [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: 10/06/2023] [Revised: 11/19/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
22
Durrant MG, Perry NT, Pai JJ, Jangid AR, Athukoralage JS, Hiraizumi M, McSpedon JP, Pawluk A, Nishimasu H, Konermann S, Hsu PD. Bridge RNAs direct modular and programmable recombination of target and donor DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577089. [PMID: 38328150 PMCID: PMC10849738 DOI: 10.1101/2024.01.24.577089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
23
Wei Q, Wang R, Jiang Y, Wei L, Sun Y, Geng J, Su R. ConPep: Prediction of peptide contact maps with pre-trained biological language model and multi-view feature extracting strategy. Comput Biol Med 2023;167:107631. [PMID: 37948966 DOI: 10.1016/j.compbiomed.2023.107631] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
24
Xie WJ, Warshel A. Harnessing generative AI to decode enzyme catalysis and evolution for enhanced engineering. Natl Sci Rev 2023;10:nwad331. [PMID: 38299119 PMCID: PMC10829072 DOI: 10.1093/nsr/nwad331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 02/02/2024]  Open
25
Qu Y, Niu Z, Ding Q, Zhao T, Kong T, Bai B, Ma J, Zhao Y, Zheng J. Ensemble Learning with Supervised Methods Based on Large-Scale Protein Language Models for Protein Mutation Effects Prediction. Int J Mol Sci 2023;24:16496. [PMID: 38003686 PMCID: PMC10671426 DOI: 10.3390/ijms242216496] [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: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]  Open
26
Li M, Wang H, Yang Z, Zhang L, Zhu Y. DeepTM: A deep learning algorithm for prediction of melting temperature of thermophilic proteins directly from sequences. Comput Struct Biotechnol J 2023;21:5544-5560. [PMID: 38034401 PMCID: PMC10681957 DOI: 10.1016/j.csbj.2023.11.006] [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: 08/23/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]  Open
27
Liu Z, Zhu YH, Shen LC, Xiao X, Qiu WR, Yu DJ. Integrating unsupervised language model with multi-view multiple sequence alignments for high-accuracy inter-chain contact prediction. Comput Biol Med 2023;166:107529. [PMID: 37748220 DOI: 10.1016/j.compbiomed.2023.107529] [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: 08/01/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 09/27/2023]
28
Qin X, Liu M, Liu G. ResCNNT-fold: Combining residual convolutional neural network and Transformer for protein fold recognition from language model embeddings. Comput Biol Med 2023;166:107571. [PMID: 37864911 DOI: 10.1016/j.compbiomed.2023.107571] [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: 08/31/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
29
Jia K, Kilinc M, Jernigan RL. New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions. FRONTIERS IN BIOINFORMATICS 2023;3:1227193. [PMID: 37900964 PMCID: PMC10602800 DOI: 10.3389/fbinf.2023.1227193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/14/2023] [Indexed: 10/31/2023]  Open
30
Xie WJ, Warshel A. Harnessing Generative AI to Decode Enzyme Catalysis and Evolution for Enhanced Engineering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561808. [PMID: 37873334 PMCID: PMC10592750 DOI: 10.1101/2023.10.10.561808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
31
Huang B, Kong L, Wang C, Ju F, Zhang Q, Zhu J, Gong T, Zhang H, Yu C, Zheng WM, Bu D. Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:913-925. [PMID: 37001856 PMCID: PMC10928435 DOI: 10.1016/j.gpb.2022.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 03/31/2023]
32
Ru Z, Wu Y, Shao J, Yin J, Qian L, Miao X. A dual-modal graph learning framework for identifying interaction events among chemical and biotech drugs. Brief Bioinform 2023;24:bbad271. [PMID: 37507113 DOI: 10.1093/bib/bbad271] [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: 03/28/2023] [Revised: 06/18/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]  Open
33
Wang H, Zang Y, Kang Y, Zhang J, Zhang L, Zhang S. ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction. Brief Bioinform 2023;24:bbad290. [PMID: 37598423 DOI: 10.1093/bib/bbad290] [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: 04/12/2023] [Revised: 06/21/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023]  Open
34
Tang YJ, Yan K, Zhang X, Tian Y, Liu B. Protein intrinsically disordered region prediction by combining neural architecture search and multi-objective genetic algorithm. BMC Biol 2023;21:188. [PMID: 37674132 PMCID: PMC10483879 DOI: 10.1186/s12915-023-01672-5] [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: 02/19/2023] [Accepted: 07/31/2023] [Indexed: 09/08/2023]  Open
35
Li J, Sawhney A, Lee JY, Liao L. Improving Inter-Helix Contact Prediction With Local 2D Topological Information. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:3001-3012. [PMID: 37155404 DOI: 10.1109/tcbb.2023.3274361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
36
Chen L, Zhang Z, Li Z, Li R, Huo R, Chen L, Wang D, Luo X, Chen K, Liao C, Zheng M. Learning protein fitness landscapes with deep mutational scanning data from multiple sources. Cell Syst 2023;14:706-721.e5. [PMID: 37591206 DOI: 10.1016/j.cels.2023.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/30/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
37
Lin P, Yan Y, Tao H, Huang SY. Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes. Nat Commun 2023;14:4935. [PMID: 37582780 PMCID: PMC10427616 DOI: 10.1038/s41467-023-40426-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/21/2023] [Indexed: 08/17/2023]  Open
38
Liu X, Duan Y, Hong X, Xie J, Liu S. Challenges in structural modeling of RNA-protein interactions. Curr Opin Struct Biol 2023;81:102623. [PMID: 37301066 DOI: 10.1016/j.sbi.2023.102623] [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: 01/31/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
39
Montezano D, Bernstein R, Copeland MM, Slusky JSG. General features of transmembrane beta barrels from a large database. Proc Natl Acad Sci U S A 2023;120:e2220762120. [PMID: 37432995 PMCID: PMC10629564 DOI: 10.1073/pnas.2220762120] [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: 12/10/2022] [Accepted: 06/03/2023] [Indexed: 07/13/2023]  Open
40
Meng Q, Guo F, Tang J. Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model. Brief Bioinform 2023:bbad217. [PMID: 37321965 DOI: 10.1093/bib/bbad217] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/18/2023] [Accepted: 05/21/2023] [Indexed: 06/17/2023]  Open
41
Durham J, Zhang J, Humphreys IR, Pei J, Cong Q. Recent advances in predicting and modeling protein-protein interactions. Trends Biochem Sci 2023;48:527-538. [PMID: 37061423 DOI: 10.1016/j.tibs.2023.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 04/17/2023]
42
Si Y, Yan C. Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models. Brief Bioinform 2023;24:7033302. [PMID: 36759333 DOI: 10.1093/bib/bbad039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023]  Open
43
Karamanos TK. Chasing long-range evolutionary couplings in the AlphaFold era. Biopolymers 2023;114:e23530. [PMID: 36752285 PMCID: PMC10909459 DOI: 10.1002/bip.23530] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
44
Gu J, Xu Y, Nie Y. Role of distal sites in enzyme engineering. Biotechnol Adv 2023;63:108094. [PMID: 36621725 DOI: 10.1016/j.biotechadv.2023.108094] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/15/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
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Li M, Kang L, Xiong Y, Wang YG, Fan G, Tan P, Hong L. SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering. J Cheminform 2023;15:12. [PMID: 36737798 PMCID: PMC9898993 DOI: 10.1186/s13321-023-00688-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023]  Open
46
Lin P, Yan Y, Huang SY. DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning. Brief Bioinform 2023;24:6849483. [PMID: 36440949 DOI: 10.1093/bib/bbac499] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 11/30/2022]  Open
47
Moafinejad SN, Pandaranadar Jeyeram IPN, Jaryani F, Shirvanizadeh N, Baulin EF, Bujnicki JM. 1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes. Protein Sci 2023;32:e4503. [PMID: 36369832 PMCID: PMC9795538 DOI: 10.1002/pro.4503] [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: 08/16/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
48
Bhattacharya S, Roche R, Shuvo MH, Moussad B, Bhattacharya D. Contact-Assisted Threading in Low-Homology Protein Modeling. Methods Mol Biol 2023;2627:41-59. [PMID: 36959441 DOI: 10.1007/978-1-0716-2974-1_3] [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] [Indexed: 03/25/2023]
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Logel DY, Jaschke PR. Creating De Novo Overlapped Genes. Methods Mol Biol 2023;2553:95-120. [PMID: 36227541 DOI: 10.1007/978-1-0716-2617-7_6] [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] [Indexed: 06/16/2023]
50
Mufassirin MMM, Newton MAH, Sattar A. Artificial intelligence for template-free protein structure prediction: a comprehensive review. Artif Intell Rev 2022. [DOI: 10.1007/s10462-022-10350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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