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Pre-calculated protein structure alignments at the RCSB PDB website.

Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE.

Bioinformatics. 2010 Dec 1;26(23):2983-5. doi: 10.1093/bioinformatics/btq572. Epub 2010 Oct 10.


Detection of circular permutations within protein structures using CE-CP.

Bliven SE, Bourne PE, Prlić A.

Bioinformatics. 2015 Apr 15;31(8):1316-8. doi: 10.1093/bioinformatics/btu823. Epub 2014 Dec 12.


RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.

Quinn GB, Bi C, Christie CH, Pang K, Prlić A, Nakane T, Zardecki C, Voigt M, Berman HM, Bourne PE, Rose PW.

Bioinformatics. 2015 Jan 1;31(1):126-7. doi: 10.1093/bioinformatics/btu596. Epub 2014 Sep 2.


The RCSB Protein Data Bank: new resources for research and education.

Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE.

Nucleic Acids Res. 2013 Jan;41(Database issue):D475-82. doi: 10.1093/nar/gks1200. Epub 2012 Nov 27.


STING Millennium: A web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence.

Neshich G, Togawa RC, Mancini AL, Kuser PR, Yamagishi ME, Pappas G Jr, Torres WV, Fonseca e Campos T, Ferreira LL, Luna FM, Oliveira AG, Miura RT, Inoue MK, Horita LG, de Souza DF, Dominiquini F, Alvaro A, Lima CS, Ogawa FO, Gomes GB, Palandrani JF, dos Santos GF, de Freitas EM, Mattiuz AR, Costa IC, de Almeida CL, Souza S, Baudet C, Higa RH.

Nucleic Acids Res. 2003 Jul 1;31(13):3386-92.


The RCSB Protein Data Bank: redesigned web site and web services.

Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE.

Nucleic Acids Res. 2011 Jan;39(Database issue):D392-401. doi: 10.1093/nar/gkq1021. Epub 2010 Oct 29.


DMAPS: a database of multiple alignments for protein structures.

Guda C, Pal LR, Shindyalov IN.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D273-6.


The RCSB PDB information portal for structural genomics.

Kouranov A, Xie L, de la Cruz J, Chen L, Westbrook J, Bourne PE, Berman HM.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D302-5.


Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.

Bluhm WF, Beran B, Bi C, Dimitropoulos D, Prlic A, Quinn GB, Rose PW, Shah C, Young J, Yukich B, Berman HM, Bourne PE.

Database (Oxford). 2011 Mar 7;2011:bar003. doi: 10.1093/database/bar003. Print 2011.


ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure.

Higa RH, Montagner AJ, Togawa RC, Kuser PR, Yamagishi ME, Mancini AL, Pappas G Jr, Miura RT, Horita LG, Neshich G.

Bioinformatics. 2004 Aug 12;20(12):1983-5. Epub 2004 Mar 25.


Using the tools and resources of the RCSB protein data bank.

Dutta S, M Berman H, F Bluhm W.

Curr Protoc Bioinformatics. 2007 Dec;Chapter 1:Unit1.9. doi: 10.1002/0471250953.bi0109s20.


MATRAS: A program for protein 3D structure comparison.

Kawabata T.

Nucleic Acids Res. 2003 Jul 1;31(13):3367-9.


ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

Konc J, Cesnik T, Konc JT, Penca M, Janežič D.

J Chem Inf Model. 2012 Feb 27;52(2):604-12. doi: 10.1021/ci2005687. Epub 2012 Feb 7.


Integration of open access literature into the RCSB Protein Data Bank using BioLit.

Prlić A, Martinez MA, Dimitropoulos D, Beran B, Yukich BT, Rose PW, Bourne PE, Fink JL.

BMC Bioinformatics. 2010 Apr 29;11:220. doi: 10.1186/1471-2105-11-220.


Dali server: conservation mapping in 3D.

Holm L, Rosenström P.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W545-9. doi: 10.1093/nar/gkq366. Epub 2010 May 10.


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.


Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.


FATCAT: a web server for flexible structure comparison and structure similarity searching.

Ye Y, Godzik A.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W582-5.


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.


The Protein Data Bank: unifying the archive.

Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM.

Nucleic Acids Res. 2002 Jan 1;30(1):245-8.

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