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For: Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007;5:17. [PMID: 17488521 PMCID: PMC1878469 DOI: 10.1186/1741-7007-5-17] [Citation(s) in RCA: 341] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Accepted: 05/08/2007] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
301
Nnakwe CC, Altaf M, Côté J, Kron SJ. Dissection of Rad9 BRCT domain function in the mitotic checkpoint response to telomere uncapping. DNA Repair (Amst) 2009;8:1452-61. [PMID: 19880356 DOI: 10.1016/j.dnarep.2009.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 08/27/2009] [Accepted: 09/21/2009] [Indexed: 11/29/2022]
302
Protein structure prediction begins well but ends badly. Proteins 2009;78:1282-90. [DOI: 10.1002/prot.22646] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
303
Botelho HM, Leal SS, Veith A, Prosinecki V, Bauer C, Fröhlich R, Kletzin A, Gomes CM. Role of a novel disulfide bridge within the all-beta fold of soluble Rieske proteins. J Biol Inorg Chem 2009;15:271-81. [PMID: 19862563 DOI: 10.1007/s00775-009-0596-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 10/04/2009] [Indexed: 11/25/2022]
304
Glekas GD, Foster RM, Cates JR, Estrella JA, Wawrzyniak MJ, Rao CV, Ordal GW. A PAS domain binds asparagine in the chemotaxis receptor McpB in Bacillus subtilis. J Biol Chem 2009;285:1870-8. [PMID: 19864420 DOI: 10.1074/jbc.m109.072108] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
305
Helles G, Fonseca R. Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks. BMC Bioinformatics 2009;10:338. [PMID: 19835576 PMCID: PMC2771020 DOI: 10.1186/1471-2105-10-338] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 10/16/2009] [Indexed: 11/10/2022]  Open
306
Bultrini E, Brick K, Mukherjee S, Zhang Y, Silvestrini F, Alano P, Pizzi E. Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction. BMC Genomics 2009;10:445. [PMID: 19769795 PMCID: PMC2756283 DOI: 10.1186/1471-2164-10-445] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 09/21/2009] [Indexed: 11/24/2022]  Open
307
Li Y, Zhang Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 2009;76:665-76. [PMID: 19274737 PMCID: PMC2771173 DOI: 10.1002/prot.22380] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
308
Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol 2009;9:199. [PMID: 19671178 PMCID: PMC2739858 DOI: 10.1186/1471-2148-9-199] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 08/11/2009] [Indexed: 11/29/2022]  Open
309
Valdés JJ, Weeks OI. Lithium: a potential estrogen signaling modulator. J Appl Biomed 2009. [DOI: 10.32725/jab.2009.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
310
On the intracellular trafficking of mouse S5 ribosomal protein from cytoplasm to nucleoli. J Mol Biol 2009;392:1192-204. [PMID: 19631221 DOI: 10.1016/j.jmb.2009.07.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 07/07/2009] [Accepted: 07/16/2009] [Indexed: 11/21/2022]
311
Veith A, Klingl A, Zolghadr B, Lauber K, Mentele R, Lottspeich F, Rachel R, Albers SV, Kletzin A. Acidianus,SulfolobusandMetallosphaerasurface layers: structure, composition and gene expression. Mol Microbiol 2009;73:58-72. [DOI: 10.1111/j.1365-2958.2009.06746.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
312
New vistas in GPCR 3D structure prediction. J Mol Model 2009;16:183-91. [PMID: 19551412 DOI: 10.1007/s00894-009-0533-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
313
Weraarpachai W, Antonicka H, Sasarman F, Seeger J, Schrank B, Kolesar JE, Lochmüller H, Chevrette M, Kaufman BA, Horvath R, Shoubridge EA. Mutation in TACO1, encoding a translational activator of COX I, results in cytochrome c oxidase deficiency and late-onset Leigh syndrome. Nat Genet 2009;41:833-7. [DOI: 10.1038/ng.390] [Citation(s) in RCA: 229] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 04/27/2009] [Indexed: 12/15/2022]
314
Zhou H, Skolnick J. Protein structure prediction by pro-Sp3-TASSER. Biophys J 2009;96:2119-27. [PMID: 19289038 DOI: 10.1016/j.bpj.2008.12.3898] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 11/12/2008] [Accepted: 12/03/2008] [Indexed: 12/29/2022]  Open
315
Benkert P, Schwede T, Tosatto SC. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC STRUCTURAL BIOLOGY 2009;9:35. [PMID: 19457232 PMCID: PMC2709111 DOI: 10.1186/1472-6807-9-35] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 05/20/2009] [Indexed: 11/10/2022]
316
Benkert P, Künzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic Acids Res 2009;37:W510-4. [PMID: 19429685 DOI: 10.1093/nar/gkp322] [Citation(s) in RCA: 593] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
317
Anderson DM, Beres BJ, Wilson-Rawls J, Rawls A. The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor complex. Dev Dyn 2009;238:572-80. [PMID: 19235719 DOI: 10.1002/dvdy.21873] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
318
Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009;19:145-55. [PMID: 19327982 PMCID: PMC2673339 DOI: 10.1016/j.sbi.2009.02.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 02/18/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
319
Skolnick J, Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 2009;10:378-91. [PMID: 19324930 DOI: 10.1093/bib/bbp017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
320
Miklós I, Novák Á, Satija R, Lyngsø R, Hein J. Stochastic models of sequence evolution including insertion—deletion events. Stat Methods Med Res 2009;18:453-85. [DOI: 10.1177/0962280208099500] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
321
Sathyanarayana BK, Hahn Y, Patankar MS, Pastan I, Lee B. Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats. BMC STRUCTURAL BIOLOGY 2009;9:1. [PMID: 19128473 PMCID: PMC2628672 DOI: 10.1186/1472-6807-9-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 01/07/2009] [Indexed: 11/25/2022]
322
Protein Structure Prediction. Bioinformatics 2009. [DOI: 10.1007/978-0-387-92738-1_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
323
A Probabilistic Graphical Model for Ab Initio Folding. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2009;5541:59-73. [PMID: 23459639 PMCID: PMC3583211 DOI: 10.1007/978-3-642-02008-7_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
324
Peng J, Xu J. Boosting Protein Threading Accuracy. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2009;5541:31-45. [PMID: 22506254 DOI: 10.1007/978-3-642-02008-7_3] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
325
El-Kased RF, Koy C, Deierling T, Lorenz P, Qian Z, Li Y, Thiesen HJ, Glocker MO. Mass spectrometric and peptide chip epitope mapping of rheumatoid arthritis autoantigen RA33. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2009;15:747-759. [PMID: 19940341 DOI: 10.1255/ejms.1040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
326
Lee J, Joo K, Kim SY, Lee J. Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing. J Comput Chem 2008;29:2479-84. [PMID: 18470971 DOI: 10.1002/jcc.20995] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
327
Randall A, Baldi P. SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC STRUCTURAL BIOLOGY 2008;8:52. [PMID: 19055744 PMCID: PMC2667183 DOI: 10.1186/1472-6807-8-52] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 12/03/2008] [Indexed: 11/10/2022]
328
Momen-Roknabadi A, Sadeghi M, Pezeshk H, Marashi SA. Impact of residue accessible surface area on the prediction of protein secondary structures. BMC Bioinformatics 2008;9:357. [PMID: 18759992 PMCID: PMC2553345 DOI: 10.1186/1471-2105-9-357] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2007] [Accepted: 08/31/2008] [Indexed: 12/02/2022]  Open
329
Wu S, Zhang Y. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 2008;72:547-56. [PMID: 18247410 DOI: 10.1002/prot.21945] [Citation(s) in RCA: 276] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
330
Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J 2008;95:1956-64. [PMID: 18487301 DOI: 10.1529/biophysj.108.129759] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
331
Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008;18:342-8. [PMID: 18436442 DOI: 10.1016/j.sbi.2008.02.004] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 02/14/2008] [Indexed: 10/22/2022]
332
Helles G. A comparative study of the reported performance of ab initio protein structure prediction algorithms. J R Soc Interface 2008;5:387-96. [PMID: 18077243 DOI: 10.1098/rsif.2007.1278] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
333
Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC STRUCTURAL BIOLOGY 2008;8:18. [PMID: 18366648 PMCID: PMC2311309 DOI: 10.1186/1472-6807-8-18] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 03/17/2008] [Indexed: 11/26/2022]
334
Miklós I, Novák A, Dombai B, Hein J. How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics 2008;9:137. [PMID: 18315874 PMCID: PMC2324098 DOI: 10.1186/1471-2105-9-137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 03/03/2008] [Indexed: 11/10/2022]  Open
335
Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. ACTA ACUST UNITED AC 2008;24:924-31. [PMID: 18296462 DOI: 10.1093/bioinformatics/btn069] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
336
Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2008;69 Suppl 8:108-17. [PMID: 17894355 DOI: 10.1002/prot.21702] [Citation(s) in RCA: 338] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
337
Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008;9:40. [PMID: 18215316 PMCID: PMC2245901 DOI: 10.1186/1471-2105-9-40] [Citation(s) in RCA: 3835] [Impact Index Per Article: 239.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 01/23/2008] [Indexed: 11/10/2022]  Open
338
Chelliah V, Taylor WR. Functional site prediction selects correct protein models. BMC Bioinformatics 2008;9 Suppl 1:S13. [PMID: 18315844 PMCID: PMC2259414 DOI: 10.1186/1471-2105-9-s1-s13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
339
Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins 2007;71:1175-82. [PMID: 18004754 DOI: 10.1002/prot.21809] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
340
Kaján L, Rychlewski L. Evaluation of 3D-Jury on CASP7 models. BMC Bioinformatics 2007;8:304. [PMID: 17711571 PMCID: PMC2040163 DOI: 10.1186/1471-2105-8-304] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 08/21/2007] [Indexed: 11/10/2022]  Open
341
Zhou H, Skolnick J. Ab initio protein structure prediction using chunk-TASSER. Biophys J 2007;93:1510-8. [PMID: 17496016 PMCID: PMC1948038 DOI: 10.1529/biophysj.107.109959] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
342
Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007;35:3375-82. [PMID: 17478507 PMCID: PMC1904280 DOI: 10.1093/nar/gkm251] [Citation(s) in RCA: 591] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
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