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For: Hou J, Adhikari B, Cheng J. DeepSF: deep convolutional neural network for mapping protein sequences to folds. Bioinformatics 2019;34:1295-1303. [PMID: 29228193 PMCID: PMC5905591 DOI: 10.1093/bioinformatics/btx780] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 12/07/2017] [Indexed: 11/30/2022]  Open
Number Cited by Other Article(s)
1
Asim MN, Asif T, Hassan F, Dengel A. Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models. Database (Oxford) 2025;2025:baaf027. [PMID: 40448683 DOI: 10.1093/database/baaf027] [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: 09/28/2024] [Revised: 02/06/2025] [Accepted: 03/26/2025] [Indexed: 06/02/2025]
2
Kim S, Kim MA, Kim B, Lee J, Jung SK, Kim J, Chung HY, Lee CY, Jeong S. Machine learning assessment of zoonotic potential in avian influenza viruses using PB2 segment. BMC Genomics 2025;26:395. [PMID: 40269678 PMCID: PMC12020041 DOI: 10.1186/s12864-025-11589-8] [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: 01/16/2025] [Accepted: 04/09/2025] [Indexed: 04/25/2025]  Open
3
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
4
Yang D, Peng X, Zheng S, Peng S. Deep learning-based prediction of autoimmune diseases. Sci Rep 2025;15:4576. [PMID: 39920178 PMCID: PMC11806040 DOI: 10.1038/s41598-025-88477-4] [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: 04/01/2024] [Accepted: 01/28/2025] [Indexed: 02/09/2025]  Open
5
Wang D, Pourmirzaei M, Abbas UL, Zeng S, Manshour N, Esmaili F, Poudel B, Jiang Y, Shao Q, Chen J, Xu D. S-PLM: Structure-Aware Protein Language Model via Contrastive Learning Between Sequence and Structure. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2404212. [PMID: 39665266 PMCID: PMC11791933 DOI: 10.1002/advs.202404212] [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: 04/20/2024] [Revised: 08/21/2024] [Indexed: 12/13/2024]
6
Wang M, Wang J, Ji J, Ma C, Wang H, He J, Song Y, Zhang X, Cao Y, Dai Y, Hua M, Qin R, Li K, Cao L. Improving compound-protein interaction prediction by focusing on intra-modality and inter-modality dynamics with a multimodal tensor fusion strategy. Comput Struct Biotechnol J 2024;23:3714-3729. [PMID: 39525082 PMCID: PMC11544084 DOI: 10.1016/j.csbj.2024.10.004] [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: 06/13/2024] [Revised: 10/01/2024] [Accepted: 10/01/2024] [Indexed: 11/16/2024]  Open
7
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]
8
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
9
Tan Y, Li M, Zhou Z, Tan P, Yu H, Fan G, Hong L. PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications. J Cheminform 2024;16:92. [PMID: 39095917 PMCID: PMC11297785 DOI: 10.1186/s13321-024-00884-3] [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: 03/21/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024]  Open
10
Jamasb AR, Morehead A, Joshi CK, Zhang Z, Didi K, Mathis S, Harris C, Tang J, Cheng J, Liò P, Blundell TL. Evaluating Representation Learning on the Protein Structure Universe. ARXIV 2024:arXiv:2406.13864v1. [PMID: 38947934 PMCID: PMC11213157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
11
Nguyen VTD, Hy TS. Multimodal pretraining for unsupervised protein representation learning. Biol Methods Protoc 2024;9:bpae043. [PMID: 38983679 PMCID: PMC11233121 DOI: 10.1093/biomethods/bpae043] [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: 04/15/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]  Open
12
Dotan E, Jaschek G, Pupko T, Belinkov Y. Effect of tokenization on transformers for biological sequences. Bioinformatics 2024;40:btae196. [PMID: 38608190 PMCID: PMC11055402 DOI: 10.1093/bioinformatics/btae196] [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: 08/23/2023] [Revised: 02/20/2024] [Accepted: 04/11/2024] [Indexed: 04/14/2024]  Open
13
Ektefaie Y, Shen A, Bykova D, Marin M, Zitnik M, Farhat M. Evaluating generalizability of artificial intelligence models for molecular datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581982. [PMID: 38464295 PMCID: PMC10925170 DOI: 10.1101/2024.02.25.581982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
14
Valentini G, Malchiodi D, Gliozzo J, Mesiti M, Soto-Gomez M, Cabri A, Reese J, Casiraghi E, Robinson PN. The promises of large language models for protein design and modeling. FRONTIERS IN BIOINFORMATICS 2023;3:1304099. [PMID: 38076030 PMCID: PMC10701588 DOI: 10.3389/fbinf.2023.1304099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/07/2023] [Indexed: 10/16/2024]  Open
15
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
16
Yang M, Chen S, Huang Z, Gao S, Yu T, Du T, Zhang H, Li X, Liu CM, Chen S, Li H. Deep learning-enabled discovery and characterization of HKT genes in Spartina alterniflora. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;116:690-705. [PMID: 37494542 DOI: 10.1111/tpj.16397] [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: 04/10/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
17
Hui T, Descoteaux ML, Miao J, Lin YS. Training Neural Network Models Using Molecular Dynamics Simulation Results to Efficiently Predict Cyclic Hexapeptide Structural Ensembles. J Chem Theory Comput 2023. [PMID: 37236147 PMCID: PMC10373485 DOI: 10.1021/acs.jctc.3c00154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
18
Wu F, Courty N, Jin S, Li SZ. Improving molecular representation learning with metric learning-enhanced optimal transport. PATTERNS (NEW YORK, N.Y.) 2023;4:100714. [PMID: 37123438 PMCID: PMC10140620 DOI: 10.1016/j.patter.2023.100714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/29/2022] [Accepted: 03/01/2023] [Indexed: 05/02/2023]
19
Sanderson T, Bileschi ML, Belanger D, Colwell LJ. ProteInfer, deep neural networks for protein functional inference. eLife 2023;12:e80942. [PMID: 36847334 PMCID: PMC10063232 DOI: 10.7554/elife.80942] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/24/2023] [Indexed: 03/01/2023]  Open
20
Wang F, Feng X, Kong R, Chang S. Generating new protein sequences by using dense network and attention mechanism. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023;20:4178-4197. [PMID: 36899622 DOI: 10.3934/mbe.2023195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
21
Wu L, Yin C, Zhu J, Wu Z, He L, Xia Y, Xie S, Qin T, Liu TY. SPRoBERTa: protein embedding learning with local fragment modeling. Brief Bioinform 2022;23:6711410. [PMID: 36136367 DOI: 10.1093/bib/bbac401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]  Open
22
An J, Weng X. Collectively encoding protein properties enriches protein language models. BMC Bioinformatics 2022;23:467. [DOI: 10.1186/s12859-022-05031-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/31/2022] [Indexed: 11/10/2022]  Open
23
Wu F, Jin S, Jiang Y, Jin X, Tang B, Niu Z, Liu X, Zhang Q, Zeng X, Li SZ. Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022;9:e2203796. [PMID: 36202759 PMCID: PMC9685463 DOI: 10.1002/advs.202203796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/07/2022] [Indexed: 05/16/2023]
24
Controllable protein design with language models. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00499-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
25
Bileschi ML, Belanger D, Bryant DH, Sanderson T, Carter B, Sculley D, Bateman A, DePristo MA, Colwell LJ. Using deep learning to annotate the protein universe. Nat Biotechnol 2022;40:932-937. [PMID: 35190689 DOI: 10.1038/s41587-021-01179-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
26
Feng G, Yao H, Li C, Liu R, Huang R, Fan X, Ge R, Miao Q. ME-ACP: Multi-view neural networks with ensemble model for identification of anticancer peptides. Comput Biol Med 2022;145:105459. [DOI: 10.1016/j.compbiomed.2022.105459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 12/26/2022]
27
Pang Y, Liu B. SelfAT-Fold: Protein Fold Recognition Based on Residue-Based and Motif-Based Self-Attention Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1861-1869. [PMID: 33090951 DOI: 10.1109/tcbb.2020.3031888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
28
Hakala K, Kaewphan S, Bjorne J, Mehryary F, Moen H, Tolvanen M, Salakoski T, Ginter F. Neural Network and Random Forest Models in Protein Function Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1772-1781. [PMID: 33306472 DOI: 10.1109/tcbb.2020.3044230] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
29
Villegas-Morcillo A, Gomez AM, Sanchez V. An analysis of protein language model embeddings for fold prediction. Brief Bioinform 2022;23:6571527. [PMID: 35443054 DOI: 10.1093/bib/bbac142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022]  Open
30
Zhang J, Yan K, Chen Q, Liu B. PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning. Bioinformatics 2022;38:2135-2143. [PMID: 35176130 DOI: 10.1093/bioinformatics/btac106] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/18/2021] [Accepted: 02/15/2022] [Indexed: 02/03/2023]  Open
31
Detlefsen NS, Hauberg S, Boomsma W. Learning meaningful representations of protein sequences. Nat Commun 2022;13:1914. [PMID: 35395843 PMCID: PMC8993921 DOI: 10.1038/s41467-022-29443-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/15/2022] [Indexed: 01/27/2023]  Open
32
Dee W. LMPred: predicting antimicrobial peptides using pre-trained language models and deep learning. BIOINFORMATICS ADVANCES 2022;2:vbac021. [PMID: 36699381 PMCID: PMC9710646 DOI: 10.1093/bioadv/vbac021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/01/2022] [Accepted: 03/29/2022] [Indexed: 01/28/2023]
33
Roethel A, Biliński P, Ishikawa T. BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network. Int J Mol Sci 2022;23:2966. [PMID: 35328384 PMCID: PMC8954277 DOI: 10.3390/ijms23062966] [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: 01/15/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 01/07/2023]  Open
34
A deep learning model to detect novel pore-forming proteins. Sci Rep 2022;12:2013. [PMID: 35132124 PMCID: PMC8821639 DOI: 10.1038/s41598-022-05970-w] [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: 06/24/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022]  Open
35
Jin X, Luo X, Liu B. PHR-search: a search framework for protein remote homology detection based on the predicted protein hierarchical relationships. Brief Bioinform 2022;23:6520306. [PMID: 35134113 DOI: 10.1093/bib/bbab609] [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: 09/22/2021] [Revised: 12/14/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022]  Open
36
Rorabaugh AK, Caíno-Lores S, Johnston T, Taufer M. High frequency accuracy and loss data of random neural networks trained on image datasets. Data Brief 2022;40:107780. [PMID: 35036484 PMCID: PMC8749157 DOI: 10.1016/j.dib.2021.107780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 11/15/2022]  Open
37
Cui F, Li S, Zhang Z, Sui M, Cao C, El-Latif Hesham A, Zou Q. DeepMC-iNABP: Deep learning for multiclass identification and classification of nucleic acid-binding proteins. Comput Struct Biotechnol J 2022;20:2020-2028. [PMID: 35521556 PMCID: PMC9065708 DOI: 10.1016/j.csbj.2022.04.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/06/2022] [Accepted: 04/20/2022] [Indexed: 11/29/2022]  Open
38
Madani M, Lin K, Tarakanova A. DSResSol: A Sequence-Based Solubility Predictor Created with Dilated Squeeze Excitation Residual Networks. Int J Mol Sci 2021;22:13555. [PMID: 34948354 PMCID: PMC8704505 DOI: 10.3390/ijms222413555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]  Open
39
Villegas-Morcillo A, Gomez AM, Morales-Cordovilla JA, Sanchez V. Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2848-2854. [PMID: 32750896 DOI: 10.1109/tcbb.2020.3012732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
40
Sandaruwan PD, Wannige CT. An improved deep learning model for hierarchical classification of protein families. PLoS One 2021;16:e0258625. [PMID: 34669708 PMCID: PMC8528337 DOI: 10.1371/journal.pone.0258625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 10/01/2021] [Indexed: 12/28/2022]  Open
41
Villegas-Morcillo A, Sanchez V, Gomez AM. FoldHSphere: deep hyperspherical embeddings for protein fold recognition. BMC Bioinformatics 2021;22:490. [PMID: 34641786 PMCID: PMC8507389 DOI: 10.1186/s12859-021-04419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/29/2021] [Indexed: 12/01/2022]  Open
42
Carrillo-Cabada H, Benson J, Razavi AM, Mulligan B, Cuendet MA, Weinstein H, Taufer M, Estrada T. A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1336-1349. [PMID: 31603792 PMCID: PMC9119144 DOI: 10.1109/tcbb.2019.2945291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
43
Zhang J, Chen Q, Liu B. DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:1451-1463. [PMID: 31722485 DOI: 10.1109/tcbb.2019.2952338] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
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Sanner MF, Dieguez L, Forli S, Lis E. Improving Docking Power for Short Peptides Using Random Forest. J Chem Inf Model 2021;61:3074-3090. [PMID: 34124893 PMCID: PMC8543977 DOI: 10.1021/acs.jcim.1c00573] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Li G, Zrimec J, Ji B, Geng J, Larsbrink J, Zelezniak A, Nielsen J, Engqvist MK. Performance of Regression Models as a Function of Experiment Noise. Bioinform Biol Insights 2021;15:11779322211020315. [PMID: 34262264 PMCID: PMC8243133 DOI: 10.1177/11779322211020315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/29/2021] [Indexed: 11/21/2022]  Open
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Jin X, Liao Q, Liu B. S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection. Bioinformatics 2021;37:4321-4327. [PMID: 34170287 DOI: 10.1093/bioinformatics/btab472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/29/2021] [Accepted: 06/24/2021] [Indexed: 01/26/2023]  Open
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Jiang H, Fan X. The Two-Step Clustering Approach for Metastable States Learning. Int J Mol Sci 2021;22:6576. [PMID: 34205252 PMCID: PMC8233889 DOI: 10.3390/ijms22126576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 01/20/2023]  Open
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Sequence-Based Prediction of Transmembrane Protein Crystallization Propensity. Interdiscip Sci 2021;13:693-702. [PMID: 34143353 DOI: 10.1007/s12539-021-00448-1] [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: 12/28/2020] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
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New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies. Neural Comput Appl 2021;33:15669-15692. [PMID: 34155424 PMCID: PMC8208613 DOI: 10.1007/s00521-021-06188-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/02/2021] [Indexed: 12/13/2022]
50
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]
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