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Results: 1 to 20 of 263

1.

SALIGN: a web server for alignment of multiple protein sequences and structures.

Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.

PMID:
22618536
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.

PMID:
14681398
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

ModBase, a database of annotated comparative protein structure models, and associated resources.

Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. doi: 10.1093/nar/gkq1091. Epub 2010 Nov 19.

PMID:
21097780
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

PROMALS3D web server for accurate multiple protein sequence and structure alignments.

Pei J, Tang M, Grishin NV.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W30-4. doi: 10.1093/nar/gkn322. Epub 2008 May 24.

PMID:
18503087
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

PROMALS web server for accurate multiple protein sequence alignments.

Pei J, Kim BH, Tang M, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.

PMID:
17452345
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

DBAli tools: mining the protein structure space.

Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.

PMID:
17478513
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C.

Bioinformatics. 2006 Oct 1;22(19):2439-40.

PMID:
17032685
[PubMed - indexed for MEDLINE]
Free Article
8.

FFAS03: a server for profile--profile sequence alignments.

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8.

PMID:
15980471
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Tools for comparative protein structure modeling and analysis.

Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A.

Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.

PMID:
12824331
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information.

Pei J, Grishin NV.

Methods Mol Biol. 2014;1079:263-71. doi: 10.1007/978-1-62703-646-7_17.

PMID:
24170408
[PubMed - indexed for MEDLINE]
11.

Alignment of protein sequences by their profiles.

Marti-Renom MA, Madhusudhan MS, Sali A.

Protein Sci. 2004 Apr;13(4):1071-87.

PMID:
15044736
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

MODBASE: a database of annotated comparative protein structure models and associated resources.

Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5.

PMID:
16381869
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

ModLoop: automated modeling of loops in protein structures.

Fiser A, Sali A.

Bioinformatics. 2003 Dec 12;19(18):2500-1.

PMID:
14668246
[PubMed - indexed for MEDLINE]
Free Article
14.

MAGOS: multiple alignment and modelling server.

Garnier N, Friedrich A, Bolze R, Bettler E, Moulinier L, Geourjon C, Thompson JD, Deléage G, Poch O.

Bioinformatics. 2006 Sep 1;22(17):2164-5. Epub 2006 Jul 4.

PMID:
16820425
[PubMed - indexed for MEDLINE]
Free Article
15.

M4T: a comparative protein structure modeling server.

Fernandez-Fuentes N, Madrid-Aliste CJ, Rai BK, Fajardo JE, Fiser A.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W363-8. Epub 2007 May 21.

PMID:
17517764
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Adaptive Smith-Waterman residue match seeding for protein structural alignment.

Topham CM, Rouquier M, Tarrat N, André I.

Proteins. 2013 Oct;81(10):1823-39. doi: 10.1002/prot.24327. Epub 2013 Aug 19.

PMID:
23720362
[PubMed - indexed for MEDLINE]
17.

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T.

Bioinformatics. 2009 Aug 1;25(15):1972-3. doi: 10.1093/bioinformatics/btp348. Epub 2009 Jun 8.

PMID:
19505945
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The SSEA server for protein secondary structure alignment.

Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SC.

Bioinformatics. 2005 Feb 1;21(3):393-5. Epub 2004 Sep 3.

PMID:
15347578
[PubMed - indexed for MEDLINE]
Free Article
19.

Alignment of multiple protein structures based on sequence and structure features.

Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A.

Protein Eng Des Sel. 2009 Sep;22(9):569-74. doi: 10.1093/protein/gzp040. Epub 2009 Jul 8.

PMID:
19587024
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Elnitski L, Riemer C, Burhans R, Hardison R, Miller W.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s9.

PMID:
18428743
[PubMed - indexed for MEDLINE]
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