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For: Ofran Y, Rost B. ISIS: interaction sites identified from sequence. Bioinformatics 2007;23:e13-6. [PMID: 17237081 DOI: 10.1093/bioinformatics/btl303] [Citation(s) in RCA: 172] [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] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
51
Zhang B, Li J, Quan L, Chen Y, Lü Q. Sequence-based prediction of protein-protein interaction sites by simplified long short-term memory network. Neurocomputing 2019. [DOI: 10.1016/j.neucom.2019.05.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
52
Sarkar D, Saha S. Machine-learning techniques for the prediction of protein–protein interactions. J Biosci 2019. [DOI: 10.1007/s12038-019-9909-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
53
Reille S, Garnier M, Robert X, Gouet P, Martin J, Launay G. Identification and visualization of protein binding regions with the ArDock server. Nucleic Acids Res 2019;46:W417-W422. [PMID: 29905873 PMCID: PMC6031020 DOI: 10.1093/nar/gky472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]  Open
54
Gil N, Fajardo EJ, Fiser A. Discovery of receptor-ligand interfaces in the immunoglobulin superfamily. Proteins 2019;88:135-142. [PMID: 31298437 DOI: 10.1002/prot.25778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/13/2022]
55
Wang X, Yu B, Ma A, Chen C, Liu B, Ma Q. Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. Bioinformatics 2019;35:2395-2402. [PMID: 30520961 PMCID: PMC6612859 DOI: 10.1093/bioinformatics/bty995] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/19/2018] [Accepted: 12/03/2018] [Indexed: 11/14/2022]  Open
56
Dequeker C, Laine E, Carbone A. Decrypting protein surfaces by combining evolution, geometry, and molecular docking. Proteins 2019;87:952-965. [PMID: 31199528 PMCID: PMC6852240 DOI: 10.1002/prot.25757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/09/2019] [Accepted: 06/07/2019] [Indexed: 01/30/2023]
57
Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation. Int J Med Microbiol 2019;309:288-298. [PMID: 31126750 DOI: 10.1016/j.ijmm.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/28/2019] [Accepted: 03/17/2019] [Indexed: 12/31/2022]  Open
58
Kolvenbach CM, Dworschak GC, Frese S, Japp AS, Schuster P, Wenzlitschke N, Yilmaz Ö, Lopes FM, Pryalukhin A, Schierbaum L, van der Zanden LFM, Kause F, Schneider R, Taranta-Janusz K, Szczepańska M, Pawlaczyk K, Newman WG, Beaman GM, Stuart HM, Cervellione RM, Feitz WFJ, van Rooij IALM, Schreuder MF, Steffens M, Weber S, Merz WM, Feldkötter M, Hoppe B, Thiele H, Altmüller J, Berg C, Kristiansen G, Ludwig M, Reutter H, Woolf AS, Hildebrandt F, Grote P, Zaniew M, Odermatt B, Hilger AC. Rare Variants in BNC2 Are Implicated in Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction. Am J Hum Genet 2019;104:994-1006. [PMID: 31051115 PMCID: PMC6506863 DOI: 10.1016/j.ajhg.2019.03.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/22/2019] [Indexed: 12/29/2022]  Open
59
Zhang X, Lin X, Zhao J, Huang Q, Xu X. Efficiently Predicting Hot Spots in PPIs by Combining Random Forest and Synthetic Minority Over-Sampling Technique. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:774-781. [PMID: 33156780 DOI: 10.1109/tcbb.2018.2871674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
60
Improved measures for evolutionary conservation that exploit taxonomy distances. Nat Commun 2019;10:1556. [PMID: 30952844 PMCID: PMC6450959 DOI: 10.1038/s41467-019-09583-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 03/19/2019] [Indexed: 11/30/2022]  Open
61
Emamjomeh A, Choobineh D, Hajieghrari B, MahdiNezhad N, Khodavirdipour A. DNA-protein interaction: identification, prediction and data analysis. Mol Biol Rep 2019;46:3571-3596. [PMID: 30915687 DOI: 10.1007/s11033-019-04763-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022]
62
Lipinski S, Petersen BS, Barann M, Piecyk A, Tran F, Mayr G, Jentzsch M, Aden K, Stengel ST, Klostermeier UC, Sheth V, Ellinghaus D, Rausch T, Korbel JO, Nothnagel M, Krawczak M, Gilissen C, Veltman JA, Forster M, Forster P, Lee CC, Fritscher-Ravens A, Schreiber S, Franke A, Rosenstiel P. Missense variants in NOX1 and p22phox in a case of very-early-onset inflammatory bowel disease are functionally linked to NOD2. Cold Spring Harb Mol Case Stud 2019;5:mcs.a002428. [PMID: 30709874 PMCID: PMC6371741 DOI: 10.1101/mcs.a002428] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 10/29/2018] [Indexed: 02/07/2023]  Open
63
Bakhman A, Rabinovich E, Shlamkovich T, Papo N, Kosloff M. Residue-level determinants of angiopoietin-2 interactions with its receptor Tie2. Proteins 2018;87:185-197. [PMID: 30520519 DOI: 10.1002/prot.25638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/04/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
64
The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Sci Rep 2018;8:17875. [PMID: 30552341 PMCID: PMC6294744 DOI: 10.1038/s41598-018-35756-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/08/2018] [Indexed: 12/02/2022]  Open
65
Compound heterozygous mutations in IL10RA combined with a complement factor properdin mutation in infantile-onset inflammatory bowel disease. Eur J Gastroenterol Hepatol 2018;30:1491-1496. [PMID: 30199474 DOI: 10.1097/meg.0000000000001247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
66
Macalino SJY, Basith S, Clavio NAB, Chang H, Kang S, Choi S. Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. Molecules 2018;23:E1963. [PMID: 30082644 PMCID: PMC6222862 DOI: 10.3390/molecules23081963] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022]  Open
67
Vikram T, Kumar P. Analysis of Hepatitis E virus (HEV) X-domain structural model. Bioinformation 2018;14:398-403. [PMID: 30262978 PMCID: PMC6143357 DOI: 10.6026/97320630014398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 06/26/2018] [Accepted: 06/30/2018] [Indexed: 01/22/2023]  Open
68
Atas H, Tuncbag N, Doğan T. Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. Methods Mol Biol 2018;1762:51-69. [PMID: 29594767 DOI: 10.1007/978-1-4939-7756-7_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
69
Nadaradjane AA, Guerois R, Andreani J. Protein-Protein Docking Using Evolutionary Information. Methods Mol Biol 2018;1764:429-447. [PMID: 29605932 DOI: 10.1007/978-1-4939-7759-8_28] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
70
Qiu Z, Zhou B, Yuan J. Protein–protein interaction site predictions with minimum covariance determinant and Mahalanobis distance. J Theor Biol 2017;433:57-63. [DOI: 10.1016/j.jtbi.2017.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/26/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
71
Elongation factor Tu is a multifunctional and processed moonlighting protein. Sci Rep 2017;7:11227. [PMID: 28894125 PMCID: PMC5593925 DOI: 10.1038/s41598-017-10644-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/10/2017] [Indexed: 01/10/2023]  Open
72
Berry IJ, Jarocki VM, Tacchi JL, Raymond BBA, Widjaja M, Padula MP, Djordjevic SP. N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen. Sci Rep 2017;7:11063. [PMID: 28894154 PMCID: PMC5593965 DOI: 10.1038/s41598-017-11296-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022]  Open
73
Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci Rep 2017;7:10480. [PMID: 28874689 PMCID: PMC5585393 DOI: 10.1038/s41598-017-09654-8] [Citation(s) in RCA: 545] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/28/2017] [Indexed: 01/01/2023]  Open
74
Ma L, Wang DD, Zou B, Yan H. An Eigen-Binding Site Based Method for the Analysis of Anti-EGFR Drug Resistance in Lung Cancer Treatment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1187-1194. [PMID: 27187970 DOI: 10.1109/tcbb.2016.2568184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
75
Protein binding hot spots prediction from sequence only by a new ensemble learning method. Amino Acids 2017;49:1773-1785. [DOI: 10.1007/s00726-017-2474-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/24/2017] [Indexed: 01/31/2023]
76
Tahir M, Hayat M. Machine learning based identification of protein–protein interactions using derived features of physiochemical properties and evolutionary profiles. Artif Intell Med 2017;78:61-71. [DOI: 10.1016/j.artmed.2017.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/09/2017] [Accepted: 06/11/2017] [Indexed: 02/09/2023]
77
Murakami Y, Tripathi LP, Prathipati P, Mizuguchi K. Network analysis and in silico prediction of protein-protein interactions with applications in drug discovery. Curr Opin Struct Biol 2017;44:134-142. [PMID: 28364585 DOI: 10.1016/j.sbi.2017.02.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 02/05/2017] [Accepted: 02/23/2017] [Indexed: 11/29/2022]
78
Zhang J, Kurgan L. Review and comparative assessment of sequence-based predictors of protein-binding residues. Brief Bioinform 2017;19:821-837. [DOI: 10.1093/bib/bbx022] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Indexed: 12/31/2022]  Open
79
Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;128:33-38. [PMID: 28069340 DOI: 10.1016/j.pbiomolbio.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/09/2023]
80
Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes. Methods Mol Biol 2017;1484:237-253. [PMID: 27787830 DOI: 10.1007/978-1-4939-6406-2_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
81
Ren J, Gao F, Wu X, Lu X, Zeng L, Lv J, Su X, Luo H, Ren G. Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice. Sci Rep 2016;6:37645. [PMID: 27876888 PMCID: PMC5120289 DOI: 10.1038/srep37645] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/31/2016] [Indexed: 12/03/2022]  Open
82
Kuo TH, Li KB. Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids. Int J Mol Sci 2016;17:ijms17111788. [PMID: 27792167 PMCID: PMC5133789 DOI: 10.3390/ijms17111788] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 12/17/2022]  Open
83
Phylogenomic analysis supports a recent change in nitrate assimilation in the White-nose Syndrome pathogen, Pseudogymnoascus destructans. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
84
Wei ZS, Han K, Yang JY, Shen HB, Yu DJ. Protein–protein interaction sites prediction by ensembling SVM and sample-weighted random forests. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2016.02.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
85
Keskin O, Tuncbag N, Gursoy A. Predicting Protein–Protein Interactions from the Molecular to the Proteome Level. Chem Rev 2016;116:4884-909. [PMID: 27074302 DOI: 10.1021/acs.chemrev.5b00683] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
86
Esmaielbeiki R, Krawczyk K, Knapp B, Nebel JC, Deane CM. Progress and challenges in predicting protein interfaces. Brief Bioinform 2016;17:117-31. [PMID: 25971595 PMCID: PMC4719070 DOI: 10.1093/bib/bbv027] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/18/2015] [Indexed: 12/31/2022]  Open
87
Fellner L, Simon S, Scherling C, Witting M, Schober S, Polte C, Schmitt-Kopplin P, Keim DA, Scherer S, Neuhaus K. Evidence for the recent origin of a bacterial protein-coding, overlapping orphan gene by evolutionary overprinting. BMC Evol Biol 2015;15:283. [PMID: 26677845 PMCID: PMC4683798 DOI: 10.1186/s12862-015-0558-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/06/2015] [Indexed: 01/18/2023]  Open
88
Prediction of Protein-Protein Interaction Sites Based on Naive Bayes Classifier. Biochem Res Int 2015;2015:978193. [PMID: 26697220 PMCID: PMC4677168 DOI: 10.1155/2015/978193] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/05/2015] [Accepted: 11/12/2015] [Indexed: 11/18/2022]  Open
89
Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures. J Membr Biol 2015;249:141-53. [DOI: 10.1007/s00232-015-9856-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
90
Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. PLoS Comput Biol 2015;11:e1004461. [PMID: 26506003 PMCID: PMC4623975 DOI: 10.1371/journal.pcbi.1004461] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/08/2015] [Indexed: 12/31/2022]  Open
91
Xia B, Zhang H, Li Q, Li T. PETs: A Stable and Accurate Predictor of Protein-Protein Interacting Sites Based on Extremely-Randomized Trees. IEEE Trans Nanobioscience 2015;14:882-93. [PMID: 26529772 DOI: 10.1109/tnb.2015.2491303] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
92
Chen Y, Wang XM, Zhou L, He Y, Wang D, Qi YH, Jiang DA. Rubisco Activase Is Also a Multiple Responder to Abiotic Stresses in Rice. PLoS One 2015;10:e0140934. [PMID: 26479064 PMCID: PMC4610672 DOI: 10.1371/journal.pone.0140934] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/30/2015] [Indexed: 11/19/2022]  Open
93
Hou Q, Dutilh BE, Huynen MA, Heringa J, Feenstra KA. Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case. BMC Bioinformatics 2015;16:325. [PMID: 26449222 PMCID: PMC4599308 DOI: 10.1186/s12859-015-0758-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/30/2015] [Indexed: 11/17/2022]  Open
94
Wei ZS, Yang JY, Shen HB, Yu DJ. A Cascade Random Forests Algorithm for Predicting Protein-Protein Interaction Sites. IEEE Trans Nanobioscience 2015;14:746-60. [DOI: 10.1109/tnb.2015.2475359] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
95
Calvete O, Martinez P, Garcia-Pavia P, Benitez-Buelga C, Paumard-Hernández B, Fernandez V, Dominguez F, Salas C, Romero-Laorden N, Garcia-Donas J, Carrillo J, Perona R, Triviño JC, Andrés R, Cano JM, Rivera B, Alonso-Pulpon L, Setien F, Esteller M, Rodriguez-Perales S, Bougeard G, Frebourg T, Urioste M, Blasco MA, Benítez J. A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53-negative Li-Fraumeni-like families. Nat Commun 2015;6:8383. [PMID: 26403419 DOI: 10.1038/ncomms9383] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 08/14/2015] [Indexed: 12/30/2022]  Open
96
Mosaic composition of ribA and wspB genes flanking the virB8-D4 operon in the Wolbachia supergroup B-strain, wStr. Arch Microbiol 2015;198:53-69. [PMID: 26400107 PMCID: PMC4705124 DOI: 10.1007/s00203-015-1154-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 01/28/2023]
97
Koberg S, Mohamed MDA, Faulhaber K, Neve H, Heller KJ. Identification and characterization of cis- and trans-acting elements involved in prophage induction in Streptococcus thermophilus J34. Mol Microbiol 2015;98:535-52. [PMID: 26193959 DOI: 10.1111/mmi.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2015] [Indexed: 11/29/2022]
98
Biogeography of Nocardiopsis strains from hypersaline environments of Yunnan and Xinjiang Provinces, western China. Sci Rep 2015;5:13323. [PMID: 26289784 PMCID: PMC4542603 DOI: 10.1038/srep13323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/23/2015] [Indexed: 12/19/2022]  Open
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Thompson CM, Visick KL. Assessing the function of STAS domain protein SypA in Vibrio fischeri using a comparative analysis. Front Microbiol 2015;6:760. [PMID: 26284045 PMCID: PMC4517449 DOI: 10.3389/fmicb.2015.00760] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/13/2015] [Indexed: 01/15/2023]  Open
100
Hecht M, Bromberg Y, Rost B. Better prediction of functional effects for sequence variants. BMC Genomics 2015;16 Suppl 8:S1. [PMID: 26110438 PMCID: PMC4480835 DOI: 10.1186/1471-2164-16-s8-s1] [Citation(s) in RCA: 403] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
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