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For: 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] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 08/21/2007] [Indexed: 11/10/2022]  Open
Number Cited by Other Article(s)
1
Jing X, Dong Q. MQAPRank: improved global protein model quality assessment by learning-to-rank. BMC Bioinformatics 2017;18:275. [PMID: 28545390 PMCID: PMC5445322 DOI: 10.1186/s12859-017-1691-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/16/2017] [Indexed: 11/10/2022]  Open
2
Jing X, Wang K, Lu R, Dong Q. Sorting protein decoys by machine-learning-to-rank. Sci Rep 2016;6:31571. [PMID: 27530967 PMCID: PMC4987638 DOI: 10.1038/srep31571] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/26/2016] [Indexed: 11/18/2022]  Open
3
Moustafa IM, Uchida A, Wang Y, Yennawar N, Cameron CE. Structural models of mammalian mitochondrial transcription factor B2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015;1849:987-1002. [PMID: 26066983 DOI: 10.1016/j.bbagrm.2015.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 11/26/2022]
4
Cao R, Wang Z, Cheng J. Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment. BMC STRUCTURAL BIOLOGY 2014;14:13. [PMID: 24731387 PMCID: PMC3996498 DOI: 10.1186/1472-6807-14-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 04/01/2014] [Indexed: 11/10/2022]
5
Kia A, Darve E. The accuracy of the CHARMM22/CMAP and AMBER ff99SB force fields for modelling the antimicrobial peptide cecropin P1. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.781599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
6
Yeh TY, Kowalska AK, Scipioni BR, Cheong FKY, Zheng M, Derewenda U, Derewenda ZS, Schroer TA. Dynactin helps target Polo-like kinase 1 to kinetochores via its left-handed beta-helical p27 subunit. EMBO J 2013;32:1023-35. [PMID: 23455152 PMCID: PMC3616283 DOI: 10.1038/emboj.2013.30] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 01/27/2013] [Indexed: 01/08/2023]  Open
7
Rusu M, Bonneau R, Holbrook MR, Watowich SJ, Birmanns S, Wriggers W, Freiberg AN. An assembly model of rift valley Fever virus. Front Microbiol 2012;3:254. [PMID: 22837754 PMCID: PMC3400131 DOI: 10.3389/fmicb.2012.00254] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/29/2012] [Indexed: 11/13/2022]  Open
8
Alonso-del-Rivero M, Trejo SA, Reytor ML, Rodriguez-de-la-Vega M, Delfin J, Diaz J, González-González Y, Canals F, Chavez MA, Aviles FX. Tri-domain bifunctional inhibitor of metallocarboxypeptidases A and serine proteases isolated from marine annelid Sabellastarte magnifica. J Biol Chem 2012;287:15427-38. [PMID: 22411994 DOI: 10.1074/jbc.m111.337261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
9
Amarnath S, Kawli T, Mohanty S, Srinivasan N, Nanjundiah V. Pleiotropic roles of a ribosomal protein in Dictyostelium discoideum. PLoS One 2012;7:e30644. [PMID: 22363460 PMCID: PMC3281849 DOI: 10.1371/journal.pone.0030644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 12/20/2011] [Indexed: 11/22/2022]  Open
10
Zheng M, Cierpicki T, Burdette AJ, Utepbergenov D, Janczyk PŁ, Derewenda U, Stukenberg PT, Caldwell KA, Derewenda ZS. Structural features and chaperone activity of the NudC protein family. J Mol Biol 2011;409:722-41. [PMID: 21530541 DOI: 10.1016/j.jmb.2011.04.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 04/07/2011] [Accepted: 04/07/2011] [Indexed: 11/19/2022]
11
Yang R, Gaidamakov SA, Xie J, Lee J, Martino L, Kozlov G, Crawford AK, Russo AN, Conte MR, Gehring K, Maraia RJ. La-related protein 4 binds poly(A), interacts with the poly(A)-binding protein MLLE domain via a variant PAM2w motif, and can promote mRNA stability. Mol Cell Biol 2011;31:542-56. [PMID: 21098120 PMCID: PMC3028612 DOI: 10.1128/mcb.01162-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/05/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022]  Open
12
Adamczak R, Pillardy J, Vallat BK, Meller J. Fast geometric consensus approach for protein model quality assessment. J Comput Biol 2011;18:1807-18. [PMID: 21244273 DOI: 10.1089/cmb.2010.0170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
13
Limviphuvadh V, Chua LL, Rahim RAAB, Eisenhaber F, Maurer-Stroh S, Adhikari S. Similarity of molecular phenotype between known epilepsy gene LGI1 and disease candidate gene LGI2. BMC BIOCHEMISTRY 2010;11:39. [PMID: 20863412 PMCID: PMC2949613 DOI: 10.1186/1471-2091-11-39] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 09/24/2010] [Indexed: 11/20/2022]
14
Sagemark J, Kraulis P, Weigelt J. A software tool to accelerate design of protein constructs for recombinant expression. Protein Expr Purif 2010;72:175-8. [PMID: 20359538 DOI: 10.1016/j.pep.2010.03.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 03/19/2010] [Accepted: 03/25/2010] [Indexed: 11/26/2022]
15
Zizlsperger N, Keating AE. Specific coiled-coil interactions contribute to a global model of the structure of the spindle pole body. J Struct Biol 2010;170:246-56. [PMID: 20139001 DOI: 10.1016/j.jsb.2010.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/22/2010] [Accepted: 01/23/2010] [Indexed: 11/26/2022]
16
Innate immune detection of the type III secretion apparatus through the NLRC4 inflammasome. Proc Natl Acad Sci U S A 2010;107:3076-80. [PMID: 20133635 DOI: 10.1073/pnas.0913087107] [Citation(s) in RCA: 608] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
17
Malygin AA, Bondarenko EI, Ivanisenko VA, Protopopova EV, Karpova GG, Loktev VB. C-terminal fragment of human laminin-binding protein contains a receptor domain for Venezuelan equine encephalitis and tick-borne encephalitis viruses. BIOCHEMISTRY (MOSCOW) 2010;74:1328-36. [DOI: 10.1134/s0006297909120050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
18
Elhefnawi MM, Youssif AA, Ghalwash AZ, Behaidy WHE. An integrated methodology for mining promiscuous proteins: a case study of an integrative bioinformatics approach for hepatitis C virus non-structural 5A protein. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010;680:299-305. [PMID: 20865513 DOI: 10.1007/978-1-4419-5913-3_34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
19
El Hefnawi MM, El Behaidy WH, Youssif AA, Ghalwash AZ, El Housseiny LA, Zada S. Natural genetic engineering of hepatitis C virus NS5A for immune system counterattack. Ann N Y Acad Sci 2009;1178:173-85. [PMID: 19845637 DOI: 10.1111/j.1749-6632.2009.05003.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
20
Deng X, Eickholt J, Cheng J. PreDisorder: ab initio sequence-based prediction of protein disordered regions. BMC Bioinformatics 2009;10:436. [PMID: 20025768 PMCID: PMC3087350 DOI: 10.1186/1471-2105-10-436] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/21/2009] [Indexed: 11/10/2022]  Open
21
McGuffin LJ, Roche DB. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics 2009;26:182-8. [PMID: 19897565 DOI: 10.1093/bioinformatics/btp629] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
22
Wang Z, Tegge AN, Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 2009;75:638-47. [PMID: 19004001 DOI: 10.1002/prot.22275] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
23
Kinch LN, Yarbrough ML, Orth K, Grishin NV. Fido, a novel AMPylation domain common to fic, doc, and AvrB. PLoS One 2009;4:e5818. [PMID: 19503829 PMCID: PMC2686095 DOI: 10.1371/journal.pone.0005818] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 05/07/2009] [Indexed: 11/19/2022]  Open
24
Suzuki Y, Ogawa S, Sakakibara Y. Chaperone therapy for neuronopathic lysosomal diseases: competitive inhibitors as chemical chaperones for enhancement of mutant enzyme activities. PERSPECTIVES IN MEDICINAL CHEMISTRY 2009;3:7-19. [PMID: 19812739 PMCID: PMC2754921 DOI: 10.4137/pmc.s2332] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
25
Dhar PK, Thwin CS, Tun K, Tsumoto Y, Maurer-Stroh S, Eisenhaber F, Surana U. Synthesizing non-natural parts from natural genomic template. J Biol Eng 2009;3:2. [PMID: 19187561 PMCID: PMC2642765 DOI: 10.1186/1754-1611-3-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 02/03/2009] [Indexed: 11/19/2022]  Open
26
Search for inhibitors of AminoAcyl-tRNA synthases by virtual click chemistry. J Mol Model 2008;15:665-72. [DOI: 10.1007/s00894-008-0421-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 11/07/2008] [Indexed: 11/30/2022]
27
McGuffin LJ. The ModFOLD server for the quality assessment of protein structural models. Bioinformatics 2008;24:586-7. [DOI: 10.1093/bioinformatics/btn014] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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