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For: Tang CL, Xie L, Koh IYY, Posy S, Alexov E, Honig B. On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles. J Mol Biol 2003;334:1043-62. [PMID: 14643665 DOI: 10.1016/j.jmb.2003.10.025] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Number Cited by Other Article(s)
1
Staritzbichler R, Sarti E, Yaklich E, Aleksandrova A, Stamm M, Khafizov K, Forrest LR. Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors. PLoS One 2021;16:e0239881. [PMID: 33930031 PMCID: PMC8087094 DOI: 10.1371/journal.pone.0239881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/15/2021] [Indexed: 01/08/2023]  Open
2
Fidler DR, Murphy SE, Courtis K, Antonoudiou P, El-Tohamy R, Ient J, Levine TP. Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. Traffic 2016;17:1214-1226. [PMID: 27601190 PMCID: PMC5091641 DOI: 10.1111/tra.12432] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 01/08/2023]
3
Lhota J, Hauptman R, Hart T, Ng C, Xie L. A new method to improve network topological similarity search: applied to fold recognition. Bioinformatics 2015;31:2106-14. [PMID: 25717198 DOI: 10.1093/bioinformatics/btv125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022]  Open
4
Trötschel C, Follmann M, Nettekoven JA, Mohrbach T, Forrest LR, Burkovski A, Marin K, Krämer R. Methionine uptake in Corynebacterium glutamicum by MetQNI and by MetPS, a novel methionine and alanine importer of the NSS neurotransmitter transporter family. Biochemistry 2015;47:12698-709. [PMID: 18991398 DOI: 10.1021/bi801206t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
5
Deng X, Cheng J. Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information. BMC Bioinformatics 2014;15:252. [PMID: 25062980 PMCID: PMC4133609 DOI: 10.1186/1471-2105-15-252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/17/2014] [Indexed: 11/25/2022]  Open
6
Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. Sci Rep 2014;4:5643. [PMID: 25008052 PMCID: PMC4090624 DOI: 10.1038/srep05643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/19/2014] [Indexed: 02/04/2023]  Open
7
Stamm M, Staritzbichler R, Khafizov K, Forrest LR. AlignMe--a membrane protein sequence alignment web server. Nucleic Acids Res 2014;42:W246-51. [PMID: 24753425 PMCID: PMC4086118 DOI: 10.1093/nar/gku291] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
8
Stamm M, Staritzbichler R, Khafizov K, Forrest LR. Alignment of helical membrane protein sequences using AlignMe. PLoS One 2013;8:e57731. [PMID: 23469223 PMCID: PMC3587630 DOI: 10.1371/journal.pone.0057731] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/24/2013] [Indexed: 12/20/2022]  Open
9
Kuziemko A, Honig B, Petrey D. Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol 2011;7:e1002175. [PMID: 21998567 PMCID: PMC3188491 DOI: 10.1371/journal.pcbi.1002175] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 07/14/2011] [Indexed: 11/18/2022]  Open
10
Krishnadev O, Srinivasan N. AlignHUSH: alignment of HMMs using structure and hydrophobicity information. BMC Bioinformatics 2011;12:275. [PMID: 21729312 PMCID: PMC3228556 DOI: 10.1186/1471-2105-12-275] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 07/05/2011] [Indexed: 11/10/2022]  Open
11
Xu HS, Ren WK, Liu XH, Li XQ. Aligning protein sequence and analysing substitution pattern using a class-specific matrix. J Biosci 2011;35:295-314. [PMID: 20689185 DOI: 10.1007/s12038-010-0033-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Khafizov K, Staritzbichler R, Stamm M, Forrest LR. A Study of the Evolution of Inverted-Topology Repeats from LeuT-Fold Transporters Using AlignMe. Biochemistry 2010;49:10702-13. [PMID: 21073167 DOI: 10.1021/bi101256x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Norel R, Petrey D, Honig B. PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res 2010;38:W550-4. [PMID: 20525783 PMCID: PMC2896183 DOI: 10.1093/nar/gkq475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
14
Zhu J, Cheng L, Fang Q, Zhou ZH, Honig B. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J Mol Biol 2010;397:835-51. [PMID: 20109465 DOI: 10.1016/j.jmb.2010.01.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 01/04/2010] [Accepted: 01/20/2010] [Indexed: 11/16/2022]
15
Schushan M, Xiang M, Bogomiakov P, Padan E, Rao R, Ben-Tal N. Model-guided mutagenesis drives functional studies of human NHA2, implicated in hypertension. J Mol Biol 2010;396:1181-96. [PMID: 20053353 DOI: 10.1016/j.jmb.2009.12.055] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 12/22/2009] [Accepted: 12/27/2009] [Indexed: 11/18/2022]
16
The WD40 domain is required for LRRK2 neurotoxicity. PLoS One 2009;4:e8463. [PMID: 20041156 PMCID: PMC2794542 DOI: 10.1371/journal.pone.0008463] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/24/2009] [Indexed: 11/19/2022]  Open
17
Mooney C, Pollastri G. Beyond the Twilight Zone: Automated prediction of structural properties of proteins by recursive neural networks and remote homology information. Proteins 2009;77:181-90. [DOI: 10.1002/prot.22429] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
18
Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 2008;72:1171-88. [PMID: 18338384 PMCID: PMC2761145 DOI: 10.1002/prot.22005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
19
Kundrotas PJ, Lensink MF, Alexov E. Homology-based modeling of 3D structures of protein–protein complexes using alignments of modified sequence profiles. Int J Biol Macromol 2008;43:198-208. [DOI: 10.1016/j.ijbiomac.2008.05.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Revised: 05/09/2008] [Accepted: 05/12/2008] [Indexed: 11/25/2022]
20
Targeted deletion in the beta20-beta21 loop of HIV envelope glycoprotein gp120 exposes the CD4 binding site for antibody binding. Virology 2008;377:330-8. [PMID: 18519142 DOI: 10.1016/j.virol.2008.03.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/03/2008] [Accepted: 03/28/2008] [Indexed: 11/20/2022]
21
Posy S, Shapiro L, Honig B. Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? J Mol Biol 2008;378:954-68. [PMID: 18395225 PMCID: PMC2435303 DOI: 10.1016/j.jmb.2008.02.063] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 02/06/2008] [Accepted: 02/27/2008] [Indexed: 11/19/2022]
22
Bennett-Lovsey RM, Herbert AD, Sternberg MJE, Kelley LA. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins 2008;70:611-25. [PMID: 17876813 DOI: 10.1002/prot.21688] [Citation(s) in RCA: 340] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
23
Tai K, Fowler P, Mokrab Y, Stansfeld P, Sansom MSP. Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms. Methods Cell Biol 2008;90:233-65. [PMID: 19195554 DOI: 10.1016/s0091-679x(08)00812-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
24
Protein Structure Prediction. Bioinformatics 2008;453:33-85. [DOI: 10.1007/978-1-60327-429-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
25
Landau M, Herz K, Padan E, Ben-Tal N. Model Structure of the Na+/H+ Exchanger 1 (NHE1). J Biol Chem 2007;282:37854-63. [DOI: 10.1074/jbc.m705460200] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
26
Improving pairwise sequence alignment between distantly related proteins. Methods Mol Biol 2007. [PMID: 17993679 DOI: 10.1007/978-1-59745-514-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
27
Kundrotas P, Georgieva P, Shosheva A, Christova P, Alexov E. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families. J Bioinform Comput Biol 2007;5:693-715. [PMID: 17688312 DOI: 10.1142/s0219720007002709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2006] [Accepted: 02/06/2007] [Indexed: 11/18/2022]
28
Liu S, Zhang C, Liang S, Zhou Y. Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins 2007;68:636-45. [PMID: 17510969 DOI: 10.1002/prot.21459] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
29
Mirkovic N, Li Z, Parnassa A, Murray D. Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization. Proteins 2007;66:766-77. [PMID: 17154423 DOI: 10.1002/prot.21191] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
30
Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B. Membrane protein prediction methods. Methods 2007;41:460-74. [PMID: 17367718 PMCID: PMC1934899 DOI: 10.1016/j.ymeth.2006.07.026] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 07/05/2006] [Indexed: 10/23/2022]  Open
31
Shah AR, Oehmen CS, Harper J, Webb-Robertson BJM. Integrating subcellular location for improving machine learning models of remote homology detection in eukaryotic organisms. Comput Biol Chem 2007;31:138-42. [PMID: 17416337 DOI: 10.1016/j.compbiolchem.2007.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 02/20/2007] [Indexed: 11/30/2022]
32
Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering. Proteins 2006;65:463-79. [PMID: 16927337 DOI: 10.1002/prot.21085] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
33
Kosloff M, Han GW, Krishna SS, Schwarzenbacher R, Fasnacht M, Elsliger MA, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Feuerhelm J, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Johnson H, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Levin I, McMullan D, Miller MD, Morse AT, Moy K, Nigoghossian E, Okach L, Oommachen S, Page R, Paulsen J, Quijano K, Reyes R, Rife CL, Sims E, Spraggon G, Sridhar V, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) fromAgrobacterium tumefaciensat 2.0 Å resolution. Proteins 2006;65:527-37. [PMID: 16988933 DOI: 10.1002/prot.21130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
34
Scheeff ED, Bourne PE. Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 2006;7:410. [PMID: 16970830 PMCID: PMC1622756 DOI: 10.1186/1471-2105-7-410] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 09/14/2006] [Indexed: 11/30/2022]  Open
35
Johnston RJ, Copeland JW, Fasnacht M, Etchberger JF, Liu J, Honig B, Hobert O. An unusual Zn-finger/FH2 domain protein controls a left/right asymmetric neuronal fate decision in C. elegans. Development 2006;133:3317-28. [PMID: 16887832 DOI: 10.1242/dev.02494] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
36
Kundrotas PJ, Alexov E. Predicting 3D structures of transient protein-protein complexes by homology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006;1764:1498-511. [PMID: 16963323 DOI: 10.1016/j.bbapap.2006.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 07/27/2006] [Accepted: 08/03/2006] [Indexed: 11/26/2022]
37
Ohlson T, Aggarwal V, Elofsson A, MacCallum RM. Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinformatics 2006;7:357. [PMID: 16869963 PMCID: PMC1562450 DOI: 10.1186/1471-2105-7-357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Accepted: 07/25/2006] [Indexed: 11/10/2022]  Open
38
Zhou H, Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2006;58:321-8. [PMID: 15523666 PMCID: PMC1408319 DOI: 10.1002/prot.20308] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
39
Xiang Z. Advances in homology protein structure modeling. Curr Protein Pept Sci 2006;7:217-27. [PMID: 16787261 PMCID: PMC1839925 DOI: 10.2174/138920306777452312] [Citation(s) in RCA: 320] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
40
Tomii K, Hirokawa T, Motono C. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 2006;61 Suppl 7:114-121. [PMID: 16187352 DOI: 10.1002/prot.20727] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
41
Zhou H, Zhou Y. SPARKS 2 and SP3 servers in CASP6. Proteins 2006;61 Suppl 7:152-156. [PMID: 16187357 DOI: 10.1002/prot.20732] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
42
Wang J, Feng JA. NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities. Proteins 2006;58:628-37. [PMID: 15616964 DOI: 10.1002/prot.20359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
43
Dunbrack RL. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006;16:374-84. [PMID: 16713709 DOI: 10.1016/j.sbi.2006.05.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 03/22/2006] [Accepted: 05/08/2006] [Indexed: 10/24/2022]
44
Forrest LR, Tang CL, Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 2006;91:508-17. [PMID: 16648166 PMCID: PMC1483079 DOI: 10.1529/biophysj.106.082313] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
45
Gong H, Rose GD. Does secondary structure determine tertiary structure in proteins? Proteins 2006;61:338-43. [PMID: 16104021 DOI: 10.1002/prot.20622] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
46
Cheng J, Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006;22:1456-63. [PMID: 16547073 DOI: 10.1093/bioinformatics/btl102] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
47
Casbon JA, Saqi MAS. On single and multiple models of protein families for the detection of remote sequence relationships. BMC Bioinformatics 2006;7:48. [PMID: 16448555 PMCID: PMC1397874 DOI: 10.1186/1471-2105-7-48] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 01/31/2006] [Indexed: 11/23/2022]  Open
48
Murray PS, Li Z, Wang J, Tang CL, Honig B, Murray D. Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. Structure 2006;13:1521-31. [PMID: 16216583 DOI: 10.1016/j.str.2005.07.010] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 07/01/2005] [Accepted: 07/09/2005] [Indexed: 11/25/2022]
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Petrey D, Honig B. Protein Structure Prediction: Inroads to Biology. Mol Cell 2005;20:811-9. [PMID: 16364908 DOI: 10.1016/j.molcel.2005.12.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Shatsky M, Nussinov R, Wolfson HJ. Optimization of multiple-sequence alignment based on multiple-structure alignment. Proteins 2005;62:209-17. [PMID: 16294339 DOI: 10.1002/prot.20665] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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