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For: Shrestha R, Fajardo E, Gil N, Fidelis K, Kryshtafovych A, Monastyrskyy B, Fiser A. Assessing the accuracy of contact predictions in CASP13. Proteins 2019;87:1058-1068. [PMID: 31587357 PMCID: PMC6851495 DOI: 10.1002/prot.25819] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/07/2023]
Number Cited by Other Article(s)
1
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
2
Yang KK, Fusi N, Lu AX. Convolutions are competitive with transformers for protein sequence pretraining. Cell Syst 2024;15:286-294.e2. [PMID: 38428432 DOI: 10.1016/j.cels.2024.01.008] [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: 02/22/2023] [Revised: 11/08/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
3
Peng CX, Liang F, Xia YH, Zhao KL, Hou MH, Zhang GJ. Recent Advances and Challenges in Protein Structure Prediction. J Chem Inf Model 2024;64:76-95. [PMID: 38109487 DOI: 10.1021/acs.jcim.3c01324] [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: 12/20/2023]
4
Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O. CovET: A covariation-evolutionary trace method that identifies protein structure-function modules. J Biol Chem 2023;299:104896. [PMID: 37290531 PMCID: PMC10338321 DOI: 10.1016/j.jbc.2023.104896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]  Open
5
Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023;21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]  Open
6
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: 6] [Impact Index Per Article: 6.0] [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
7
rMSA: a sequence search and alignment algorithm to improve RNA structure modeling. J Mol Biol 2022. [DOI: 10.1016/j.jmb.2022.167904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
8
Barger J, Adhikari B. New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3586-3594. [PMID: 34559660 DOI: 10.1109/tcbb.2021.3115053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
9
Ahmed S, Chattopadhyay G, Manjunath K, Bhasin M, Singh N, Rasool M, Das S, Rana V, Khan N, Mitra D, Asok A, Singh R, Varadarajan R. Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region. Front Mol Biosci 2022;9:997653. [PMID: 36275627 PMCID: PMC9585320 DOI: 10.3389/fmolb.2022.997653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022]  Open
10
Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN). Protein J 2022;41:468-476. [PMID: 36008645 DOI: 10.1007/s10930-022-10067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2022] [Indexed: 10/15/2022]
11
Li B, Roden DM, Capra JA. The 3D mutational constraint on amino acid sites in the human proteome. Nat Commun 2022;13:3273. [PMID: 35672414 PMCID: PMC9174330 DOI: 10.1038/s41467-022-30936-x] [Citation(s) in RCA: 2] [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: 11/05/2021] [Accepted: 05/19/2022] [Indexed: 12/16/2022]  Open
12
Newton MAH, Rahman J, Zaman R, Sattar A. Enhancing Protein Contact Map Prediction Accuracy via Ensembles of Inter-Residue Distance Predictors. Comput Biol Chem 2022;99:107700. [DOI: 10.1016/j.compbiolchem.2022.107700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/03/2022]
13
Bhattacharya N, Thomas N, Rao R, Dauparas J, Koo PK, Baker D, Song YS, Ovchinnikov S. Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022;27:34-45. [PMID: 34890134 PMCID: PMC8752338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
14
Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proc Natl Acad Sci U S A 2021;118:2110828118. [PMID: 34873061 DOI: 10.1073/pnas.2110828118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 12/26/2022]  Open
15
Hou M, Peng C, Zhou X, Zhang B, Zhang G. Multi contact-based folding method for de novo protein structure prediction. Brief Bioinform 2021;23:6445108. [PMID: 34849573 DOI: 10.1093/bib/bbab463] [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: 07/14/2021] [Revised: 09/21/2021] [Accepted: 10/10/2021] [Indexed: 11/12/2022]  Open
16
Evaluation of Deep Neural Network ProSPr for Accurate Protein Distance Predictions on CASP14 Targets. Int J Mol Sci 2021;22:ijms222312835. [PMID: 34884640 PMCID: PMC8657919 DOI: 10.3390/ijms222312835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/02/2022]  Open
17
Si Y, Yan C. Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function. Brief Bioinform 2021;22:6357883. [PMID: 34448830 DOI: 10.1093/bib/bbab341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/10/2021] [Accepted: 08/02/2021] [Indexed: 11/12/2022]  Open
18
Ruiz-Serra V, Pontes C, Milanetti E, Kryshtafovych A, Lepore R, Valencia A. Assessing the accuracy of contact and distance predictions in CASP14. Proteins 2021;89:1888-1900. [PMID: 34595772 DOI: 10.1002/prot.26248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/06/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022]
19
Kong L, Ju F, Zhang H, Sun S, Bu D. FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC Bioinformatics 2021;22:439. [PMID: 34525939 PMCID: PMC8444573 DOI: 10.1186/s12859-021-04353-8] [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: 06/24/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022]  Open
20
Shen T, Wu J, Lan H, Zheng L, Pei J, Wang S, Liu W, Huang J. When homologous sequences meet structural decoys: Accurate contact prediction by tFold in CASP14-(tFold for CASP14 contact prediction). Proteins 2021;89:1901-1910. [PMID: 34473376 DOI: 10.1002/prot.26232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022]
21
Wang L, Liu J, Xia Y, Xu J, Zhou X, Zhang G. Distance-guided protein folding based on generalized descent direction. Brief Bioinform 2021;22:6341661. [PMID: 34355233 DOI: 10.1093/bib/bbab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/25/2022]  Open
22
Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. CELL REPORTS METHODS 2021;1:100014. [PMID: 34355210 PMCID: PMC8336924 DOI: 10.1016/j.crmeth.2021.100014] [Citation(s) in RCA: 245] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
23
Adiyaman R, McGuffin LJ. ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Res 2021;49:W589-W596. [PMID: 34009387 PMCID: PMC8218204 DOI: 10.1093/nar/gkab300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]  Open
24
Li B, Mendenhall J, Capra JA, Meiler J. A Multitask Deep-Learning Method for Predicting Membrane Associations and Secondary Structures of Proteins. J Proteome Res 2021;20:4089-4100. [PMID: 34236204 PMCID: PMC8650144 DOI: 10.1021/acs.jproteome.1c00410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
25
Zhao KL, Liu J, Zhou XG, Su JZ, Zhang Y, Zhang GJ. MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics 2021;37:4350-4356. [PMID: 34185079 DOI: 10.1093/bioinformatics/btab484] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 11/12/2022]  Open
26
van Noort CW, Honorato RV, Bonvin AMJJ. Information-driven modeling of biomolecular complexes. Curr Opin Struct Biol 2021;70:70-77. [PMID: 34139639 DOI: 10.1016/j.sbi.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 11/15/2022]
27
DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning. Sci Rep 2021;11:12295. [PMID: 34112907 PMCID: PMC8192766 DOI: 10.1038/s41598-021-91827-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022]  Open
28
Bottino GF, Ferrari AJR, Gozzo FC, Martínez L. Structural discrimination analysis for constraint selection in protein modeling. Bioinformatics 2021;37:3766-3773. [PMID: 34086840 DOI: 10.1093/bioinformatics/btab425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 11/12/2022]  Open
29
Di Lena P, Baldi P. Fold recognition by scoring protein maps using the congruence coefficient. Bioinformatics 2021;37:506-513. [PMID: 32976564 DOI: 10.1093/bioinformatics/btaa833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 11/14/2022]  Open
30
Zhang H, Bei Z, Xi W, Hao M, Ju Z, Saravanan KM, Zhang H, Guo N, Wei Y. Evaluation of residue-residue contact prediction methods: From retrospective to prospective. PLoS Comput Biol 2021;17:e1009027. [PMID: 34029314 PMCID: PMC8177648 DOI: 10.1371/journal.pcbi.1009027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 04/28/2021] [Indexed: 12/31/2022]  Open
31
Xu J, Mcpartlon M, Li J. Improved protein structure prediction by deep learning irrespective of co-evolution information. NAT MACH INTELL 2021;3:601-609. [PMID: 34368623 PMCID: PMC8340610 DOI: 10.1038/s42256-021-00348-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
32
Li J, Xu J. Study of Real-Valued Distance Prediction for Protein Structure Prediction with Deep Learning. Bioinformatics 2021;37:3197-3203. [PMID: 33961022 PMCID: PMC8504618 DOI: 10.1093/bioinformatics/btab333] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/07/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022]  Open
33
Billings WM, Morris CJ, Della Corte D. The whole is greater than its parts: ensembling improves protein contact prediction. Sci Rep 2021;11:8039. [PMID: 33850214 PMCID: PMC8044223 DOI: 10.1038/s41598-021-87524-0] [Citation(s) in RCA: 3] [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: 01/18/2021] [Accepted: 03/29/2021] [Indexed: 11/30/2022]  Open
34
Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. PLoS Comput Biol 2021;17:e1008865. [PMID: 33770072 PMCID: PMC8026059 DOI: 10.1371/journal.pcbi.1008865] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/07/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022]  Open
35
Chen C, Wu T, Guo Z, Cheng J. Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction. Proteins 2021;89:697-707. [PMID: 33538038 PMCID: PMC8089057 DOI: 10.1002/prot.26052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/22/2020] [Accepted: 01/31/2021] [Indexed: 12/17/2022]
36
Heo L, Arbour CF, Janson G, Feig M. Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation. J Chem Theory Comput 2021;17:1931-1943. [PMID: 33562962 DOI: 10.1021/acs.jctc.0c01238] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
37
Adhikari B, Shrestha B, Bernardini M, Hou J, Lea J. DISTEVAL: a web server for evaluating predicted protein distances. BMC Bioinformatics 2021;22:8. [PMID: 33407077 PMCID: PMC7788990 DOI: 10.1186/s12859-020-03938-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 06/30/2024]  Open
38
Hameduh T, Haddad Y, Adam V, Heger Z. Homology modeling in the time of collective and artificial intelligence. Comput Struct Biotechnol J 2020;18:3494-3506. [PMID: 33304450 PMCID: PMC7695898 DOI: 10.1016/j.csbj.2020.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]  Open
39
Li B, Yang YT, Capra JA, Gerstein MB. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput Biol 2020;16:e1008291. [PMID: 33253214 PMCID: PMC7728386 DOI: 10.1371/journal.pcbi.1008291] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 12/10/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022]  Open
40
Wen B, Zeng W, Liao Y, Shi Z, Savage SR, Jiang W, Zhang B. Deep Learning in Proteomics. Proteomics 2020;20:e1900335. [PMID: 32939979 PMCID: PMC7757195 DOI: 10.1002/pmic.201900335] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/14/2020] [Indexed: 12/17/2022]
41
Aderinwale T, Christoffer CW, Sarkar D, Alnabati E, Kihara D. Computational structure modeling for diverse categories of macromolecular interactions. Curr Opin Struct Biol 2020;64:1-8. [PMID: 32599506 PMCID: PMC7665979 DOI: 10.1016/j.sbi.2020.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/23/2023]
42
Du Z, Pan S, Wu Q, Peng Z, Yang J. CATHER: a novel threading algorithm with predicted contacts. Bioinformatics 2020;36:2119-2125. [PMID: 31790141 DOI: 10.1093/bioinformatics/btz876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/31/2019] [Accepted: 11/28/2019] [Indexed: 11/14/2022]  Open
43
Adhikari B. A fully open-source framework for deep learning protein real-valued distances. Sci Rep 2020;10:13374. [PMID: 32770096 PMCID: PMC7414848 DOI: 10.1038/s41598-020-70181-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/23/2020] [Indexed: 11/12/2022]  Open
44
Abriata LA, Dal Peraro M. State-of-the-art web services for de novo protein structure prediction. Brief Bioinform 2020;22:5870389. [PMID: 34020540 DOI: 10.1093/bib/bbaa139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]  Open
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Sun J, Frishman D. DeepHelicon: Accurate prediction of inter-helical residue contacts in transmembrane proteins by residual neural networks. J Struct Biol 2020;212:107574. [PMID: 32663598 DOI: 10.1016/j.jsb.2020.107574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 01/16/2023]
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Chen MC, Li Y, Zhu YH, Ge F, Yu DJ. SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network. J Chem Inf Model 2020;60:3295-3303. [DOI: 10.1021/acs.jcim.9b01207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abriata LA, Dal Peraro M. Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? J Chem Inf Model 2020;60:2443-2447. [PMID: 32134661 DOI: 10.1021/acs.jcim.0c00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Bhattacharya S, Bhattacharya D. Evaluating the significance of contact maps in low-homology protein modeling using contact-assisted threading. Sci Rep 2020;10:2908. [PMID: 32076047 PMCID: PMC7031282 DOI: 10.1038/s41598-020-59834-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/04/2020] [Indexed: 12/02/2022]  Open
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Torrisi M, Pollastri G, Le Q. Deep learning methods in protein structure prediction. Comput Struct Biotechnol J 2020;18:1301-1310. [PMID: 32612753 PMCID: PMC7305407 DOI: 10.1016/j.csbj.2019.12.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 01/01/2023]  Open
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Guzenko D, Lafita A, Monastyrskyy B, Kryshtafovych A, Duarte JM. Assessment of protein assembly prediction in CASP13. Proteins 2019;87:1190-1199. [PMID: 31374138 DOI: 10.1002/prot.25795] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/11/2019] [Accepted: 07/27/2019] [Indexed: 01/08/2023]
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