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For: Yang J, Jang R, Zhang Y, Shen HB. High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling. ACTA ACUST UNITED AC 2013;29:2579-87. [PMID: 23946502 DOI: 10.1093/bioinformatics/btt440] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Number Cited by Other Article(s)
1
Cai J, Wang T, Deng X, Tang L, Liu L. GM-lncLoc: LncRNAs subcellular localization prediction based on graph neural network with meta-learning. BMC Genomics 2023;24:52. [PMID: 36709266 PMCID: PMC9883864 DOI: 10.1186/s12864-022-09034-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/21/2022] [Indexed: 01/29/2023]  Open
2
Gaur NK, Goyal VD, Kulkarni K, Makde RD. Machine learning classifiers aid virtual screening for efficient design of mini-protein therapeutics. Bioorg Med Chem Lett 2021;38:127852. [PMID: 33609660 DOI: 10.1016/j.bmcl.2021.127852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/15/2022]
3
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
4
Zhang GJ, Wang XQ, Ma LF, Wang LJ, Hu J, Zhou XG. Two-Stage Distance Feature-based Optimization Algorithm for De novo Protein Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:2119-2130. [PMID: 31107659 DOI: 10.1109/tcbb.2019.2917452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
5
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]
6
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]
7
Cao Z, Pan X, Yang Y, Huang Y, Shen HB. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinformatics 2019;34:2185-2194. [PMID: 29462250 DOI: 10.1093/bioinformatics/bty085] [Citation(s) in RCA: 287] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/14/2018] [Indexed: 01/01/2023]  Open
8
Jing X, Dong Q, Lu R, Dong Q. Protein Inter-Residue Contacts Prediction: Methods, Performances and Applications. Curr Bioinform 2019. [DOI: 10.2174/1574893613666181109130430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
9
Oriented covalent immobilization of recombinant protein A on the glutaraldehyde activated agarose support. Int J Biol Macromol 2018;120:100-108. [DOI: 10.1016/j.ijbiomac.2018.08.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/11/2018] [Accepted: 08/15/2018] [Indexed: 12/21/2022]
10
Zhang X, Duan Y, Han N, Wu Y. Increase in IgG-binding Capacity of Recombinant Protein a Immobilized on Heterofunctional Amino and Epoxy Agarose. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/1757-899x/381/1/012042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
11
Nikolaev D, Shtyrov AA, Panov MS, Jamal A, Chakchir OB, Kochemirovsky VA, Olivucci M, Ryazantsev MN. A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. ACS OMEGA 2018;3:7555-7566. [PMID: 30087916 PMCID: PMC6068592 DOI: 10.1021/acsomega.8b00721] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
12
Yin X, Yang J, Xiao F, Yang Y, Shen HB. MemBrain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction. NANO-MICRO LETTERS 2018;10:2. [PMID: 30393651 PMCID: PMC6199043 DOI: 10.1007/s40820-017-0156-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/26/2017] [Indexed: 05/12/2023]
13
Thangappan J, Madan B, Wu S, Lee SG. Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor. Sci Rep 2017;7:15205. [PMID: 29123217 PMCID: PMC5680341 DOI: 10.1038/s41598-017-15513-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/27/2017] [Indexed: 01/19/2023]  Open
14
Wang S, Li Z, Yu Y, Xu J. Folding Membrane Proteins by Deep Transfer Learning. Cell Syst 2017;5:202-211.e3. [PMID: 28957654 PMCID: PMC5637520 DOI: 10.1016/j.cels.2017.09.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/01/2017] [Accepted: 08/29/2017] [Indexed: 01/02/2023]
15
Wu H, Wang K, Lu L, Xue Y, Lyu Q, Jiang M. Deep Conditional Random Field Approach to Transmembrane Topology Prediction and Application to GPCR Three-Dimensional Structure Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1106-1114. [PMID: 27576262 DOI: 10.1109/tcbb.2016.2602872] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
16
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]
17
de Oliveira S, Deane C. Co-evolution techniques are reshaping the way we do structural bioinformatics. F1000Res 2017;6:1224. [PMID: 28781768 PMCID: PMC5531156 DOI: 10.12688/f1000research.11543.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 11/20/2022]  Open
18
Stahl K, Schneider M, Brock O. EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. BMC Bioinformatics 2017;18:303. [PMID: 28623886 PMCID: PMC5474060 DOI: 10.1186/s12859-017-1713-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/30/2017] [Indexed: 01/12/2023]  Open
19
Characterization of Ghrelin O-Acyltransferase (GOAT) in goldfish (Carassius auratus). PLoS One 2017;12:e0171874. [PMID: 28178327 PMCID: PMC5298278 DOI: 10.1371/journal.pone.0171874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022]  Open
20
Venko K, Roy Choudhury A, Novič M. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase. Comput Struct Biotechnol J 2017;15:232-242. [PMID: 28228927 PMCID: PMC5312651 DOI: 10.1016/j.csbj.2017.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 11/23/2022]  Open
21
Simkovic F, Thomas JMH, Keegan RM, Winn MD, Mayans O, Rigden DJ. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCRJ 2016;3:259-70. [PMID: 27437113 PMCID: PMC4937781 DOI: 10.1107/s2052252516008113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/18/2016] [Indexed: 05/05/2023]
22
Yang J, Jin QY, Zhang B, Shen HB. R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter. ACTA ACUST UNITED AC 2016;32:2435-43. [PMID: 27153618 DOI: 10.1093/bioinformatics/btw181] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/03/2016] [Indexed: 11/12/2022]
23
Morrill GA, Kostellow AB, Liu L, Gupta RK, Askari A. Evolution of the α-Subunit of Na/K-ATPase from Paramecium to Homo sapiens: Invariance of Transmembrane Helix Topology. J Mol Evol 2016;82:183-98. [PMID: 26961431 PMCID: PMC4866997 DOI: 10.1007/s00239-016-9732-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/03/2016] [Indexed: 12/01/2022]
24
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] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 11/16/2022]
25
Zhang H, Huang Q, Bei Z, Wei Y, Floudas CA. COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming. Proteins 2016;84:332-48. [PMID: 26756402 DOI: 10.1002/prot.24979] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/19/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022]
26
Shneyer BI, Ušaj M, Henn A. Myo19 is an outer mitochondrial membrane motor and effector of starvation-induced filopodia. J Cell Sci 2015;129:543-56. [PMID: 26659663 DOI: 10.1242/jcs.175349] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/05/2015] [Indexed: 12/13/2022]  Open
27
Xiao F, Shen HB. Prediction Enhancement of Residue Real-Value Relative Accessible Surface Area in Transmembrane Helical Proteins by Solving the Output Preference Problem of Machine Learning-Based Predictors. J Chem Inf Model 2015;55:2464-74. [DOI: 10.1021/acs.jcim.5b00246] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
28
Teese MG, Langosch D. Role of GxxxG Motifs in Transmembrane Domain Interactions. Biochemistry 2015;54:5125-35. [PMID: 26244771 DOI: 10.1021/acs.biochem.5b00495] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
29
Zhang J, Yang J, Jang R, Zhang Y. GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome. Structure 2015;23:1538-1549. [PMID: 26190572 DOI: 10.1016/j.str.2015.06.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/03/2015] [Accepted: 06/10/2015] [Indexed: 12/31/2022]
30
Sun HP, Huang Y, Wang XF, Zhang Y, Shen HB. Improving accuracy of protein contact prediction using balanced network deconvolution. Proteins 2015;83:485-96. [PMID: 25524593 DOI: 10.1002/prot.24744] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/20/2014] [Accepted: 12/02/2014] [Indexed: 12/28/2022]
31
Li G, Theys K, Verheyen J, Pineda-Peña AC, Khouri R, Piampongsant S, Eusébio M, Ramon J, Vandamme AM. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biol Direct 2015;10:1. [PMID: 25564011 PMCID: PMC4332441 DOI: 10.1186/s13062-014-0031-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022]  Open
32
Leman JK, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins 2015;83:1-24. [PMID: 25355688 PMCID: PMC4270820 DOI: 10.1002/prot.24703] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/01/2014] [Accepted: 10/18/2014] [Indexed: 02/06/2023]
33
Chaudhari R, Heim AJ, Li Z. Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions. J Comput Aided Mol Des 2014;29:413-20. [PMID: 25503850 DOI: 10.1007/s10822-014-9823-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 12/06/2014] [Indexed: 01/19/2023]
34
Adaptive firefly algorithm: parameter analysis and its application. PLoS One 2014;9:e112634. [PMID: 25397812 PMCID: PMC4232507 DOI: 10.1371/journal.pone.0112634] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/09/2014] [Indexed: 12/02/2022]  Open
35
Khadria AS, Mueller BK, Stefely JA, Tan CH, Pagliarini DJ, Senes A. A Gly-zipper motif mediates homodimerization of the transmembrane domain of the mitochondrial kinase ADCK3. J Am Chem Soc 2014;136:14068-77. [PMID: 25216398 PMCID: PMC4195374 DOI: 10.1021/ja505017f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
36
Hu J, He X, Yu DJ, Yang XB, Yang JY, Shen HB. A new supervised over-sampling algorithm with application to protein-nucleotide binding residue prediction. PLoS One 2014;9:e107676. [PMID: 25229688 PMCID: PMC4168127 DOI: 10.1371/journal.pone.0107676] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/09/2014] [Indexed: 12/21/2022]  Open
37
Kufareva I, Katritch V, Stevens RC, Abagyan R. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 2014;22:1120-1139. [PMID: 25066135 DOI: 10.1016/j.str.2014.06.012] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 06/05/2014] [Accepted: 06/06/2014] [Indexed: 01/22/2023]
38
Tessier D, Laroum S, Duval B, Rath EM, Church WB, Hao JK. In silico evaluation of the influence of the translocon on partitioning of membrane segments. BMC Bioinformatics 2014;15:156. [PMID: 24885988 PMCID: PMC4035737 DOI: 10.1186/1471-2105-15-156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 05/14/2014] [Indexed: 11/10/2022]  Open
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