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For: Hönigschmid P, Frishman D. Accurate prediction of helix interactions and residue contacts in membrane proteins. J Struct Biol 2016;194:112-23. [PMID: 26851352 DOI: 10.1016/j.jsb.2016.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/16/2022]
Number Cited by Other Article(s)
1
Sawhney A, Li J, Liao L. Improving AlphaFold Predicted Contacts for Alpha-Helical Transmembrane Proteins Using Structural Features. Int J Mol Sci 2024;25:5247. [PMID: 38791287 PMCID: PMC11121315 DOI: 10.3390/ijms25105247] [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: 04/12/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]  Open
2
Roterman I, Stapor K, Konieczny L. Transmembrane proteins-Different anchoring systems. Proteins 2024;92:593-609. [PMID: 38062872 DOI: 10.1002/prot.26646] [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: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/17/2023] [Indexed: 04/13/2024]
3
Faiz M, Khan SJ, Azim F, Ejaz N. Disclosing the locale of transmembrane proteins within cellular alcove by machine learning approach: systematic review and meta analysis. J Biomol Struct Dyn 2023;42:11133-11148. [PMID: 37768108 DOI: 10.1080/07391102.2023.2260490] [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: 02/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
4
Sun J, Kulandaisamy A, Ru J, Gromiha MM, Cribbs AP. TMKit: a Python interface for computational analysis of transmembrane proteins. Brief Bioinform 2023;24:bbad288. [PMID: 37594311 PMCID: PMC10516361 DOI: 10.1093/bib/bbad288] [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: 04/17/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]  Open
5
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]
6
Sun J, Ru J, Ramos-Mucci L, Qi F, Chen Z, Chen S, Cribbs AP, Deng L, Wang X. DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning. Int J Mol Sci 2023;24:1878. [PMID: 36768205 PMCID: PMC9915273 DOI: 10.3390/ijms24031878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/26/2022] [Accepted: 01/12/2023] [Indexed: 01/21/2023]  Open
7
De-Simone SG, Napoleão-Pêgo P, Gonçalves PS, Lechuga GC, Mandonado A, Graeff-Teixeira C, Provance DW. Angiostrongilus cantonensis an Atypical Presenilin: Epitope Mapping, Characterization, and Development of an ELISA Peptide Assay for Specific Diagnostic of Angiostrongyliasis. MEMBRANES 2022;12:membranes12020108. [PMID: 35207030 PMCID: PMC8878667 DOI: 10.3390/membranes12020108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/10/2022]
8
Sun J, Frishman D. Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning. Comput Struct Biotechnol J 2021;19:1512-1530. [PMID: 33815689 PMCID: PMC7985279 DOI: 10.1016/j.csbj.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/10/2022]  Open
9
Lechuga GC, Napoleão-Pêgo P, Bottino CCG, Pinho RT, Provance-Jr DW, De-Simone SG. Trypanosoma cruzi Presenilin-Like Transmembrane Aspartyl Protease: Characterization and Cellular Localization. Biomolecules 2020;10:biom10111564. [PMID: 33212923 PMCID: PMC7698364 DOI: 10.3390/biom10111564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023]  Open
10
Zhang Q, Zhu J, Ju F, Kong L, Sun S, Zheng WM, Bu D. ISSEC: inferring contacts among protein secondary structure elements using deep object detection. BMC Bioinformatics 2020;21:503. [PMID: 33153432 PMCID: PMC7643357 DOI: 10.1186/s12859-020-03793-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/30/2020] [Indexed: 11/12/2022]  Open
11
Xiao Y, Zeng B, Berner N, Frishman D, Langosch D, George Teese M. Experimental determination and data-driven prediction of homotypic transmembrane domain interfaces. Comput Struct Biotechnol J 2020;18:3230-3242. [PMID: 33209210 PMCID: PMC7649602 DOI: 10.1016/j.csbj.2020.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/22/2022]  Open
12
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: 0.8] [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]
13
Hönigschmid P, Breimann S, Weigl M, Frishman D. AllesTM: predicting multiple structural features of transmembrane proteins. BMC Bioinformatics 2020;21:242. [PMID: 32532211 PMCID: PMC7291640 DOI: 10.1186/s12859-020-03581-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/03/2020] [Indexed: 12/04/2022]  Open
14
Fang C, Jia Y, Hu L, Lu Y, Wang H. IMPContact: An Interhelical Residue Contact Prediction Method. BIOMED RESEARCH INTERNATIONAL 2020;2020:4569037. [PMID: 32309431 PMCID: PMC7140131 DOI: 10.1155/2020/4569037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/09/2020] [Indexed: 11/17/2022]
15
Feng SH, Zhang WX, Yang J, Yang Y, Shen HB. Topology Prediction Improvement of α-helical Transmembrane Proteins Through Helix-tail Modeling and Multiscale Deep Learning Fusion. J Mol Biol 2020;432:1279-1296. [DOI: 10.1016/j.jmb.2019.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/18/2022]
16
Batra V, Maheshwarappa A, Dagar K, Kumar S, Soni A, Kumaresan A, Kumar R, Datta TK. Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis). BMC Evol Biol 2019;19:214. [PMID: 31771505 PMCID: PMC6878701 DOI: 10.1186/s12862-019-1535-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 10/22/2019] [Indexed: 12/13/2022]  Open
17
Lu C, Liu Z, Zhang E, He F, Ma Z, Wang H. MPLs-Pred: Predicting Membrane Protein-Ligand Binding Sites Using Hybrid Sequence-Based Features and Ligand-Specific Models. Int J Mol Sci 2019;20:ijms20133120. [PMID: 31247932 PMCID: PMC6651575 DOI: 10.3390/ijms20133120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/23/2019] [Accepted: 06/23/2019] [Indexed: 02/07/2023]  Open
18
Zeng B, Hönigschmid P, Frishman D. Residue co-evolution helps predict interaction sites in α-helical membrane proteins. J Struct Biol 2019;206:156-169. [DOI: 10.1016/j.jsb.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/30/2019] [Accepted: 02/13/2019] [Indexed: 11/29/2022]
19
Kulandaisamy A, Priya SB, Sakthivel R, Frishman D, Gromiha MM. Statistical analysis of disease‐causing and neutral mutations in human membrane proteins. Proteins 2019;87:452-466. [DOI: 10.1002/prot.25667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/16/2019] [Accepted: 01/31/2019] [Indexed: 11/11/2022]
20
Xiong D, Mao W, Gong H. Predicting the helix-helix interactions from correlated residue mutations. Proteins 2017;85:2162-2169. [PMID: 28833538 DOI: 10.1002/prot.25370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/03/2017] [Accepted: 08/13/2017] [Indexed: 12/30/2022]
21
Simkovic F, Ovchinnikov S, Baker D, Rigden DJ. Applications of contact predictions to structural biology. IUCRJ 2017;4:291-300. [PMID: 28512576 PMCID: PMC5414403 DOI: 10.1107/s2052252517005115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
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