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Items: 1 to 20 of 99

1.

BioJava: an open-source framework for bioinformatics in 2012.

Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.

Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494.

2.

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397.

3.
4.

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.

5.

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW.

Bioinformatics. 2017 Feb 17. doi: 10.1093/bioinformatics/btx101. [Epub ahead of print]

PMID:
28334105
6.

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.

7.

Jalview Version 2--a multiple sequence alignment editor and analysis workbench.

Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ.

Bioinformatics. 2009 May 1;25(9):1189-91. doi: 10.1093/bioinformatics/btp033.

8.

Sambamba: fast processing of NGS alignment formats.

Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P.

Bioinformatics. 2015 Jun 15;31(12):2032-4. doi: 10.1093/bioinformatics/btv098.

9.

MultiSeq: unifying sequence and structure data for evolutionary analysis.

Roberts E, Eargle J, Wright D, Luthey-Schulten Z.

BMC Bioinformatics. 2006 Aug 16;7:382.

10.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

11.

geWorkbench: an open source platform for integrative genomics.

Floratos A, Smith K, Ji Z, Watkinson J, Califano A.

Bioinformatics. 2010 Jul 15;26(14):1779-80. doi: 10.1093/bioinformatics/btq282.

12.

MzJava: An open source library for mass spectrometry data processing.

Horlacher O, Nikitin F, Alocci D, Mariethoz J, Müller M, Lisacek F.

J Proteomics. 2015 Nov 3;129:63-70. doi: 10.1016/j.jprot.2015.06.013.

PMID:
26141507
13.

Prediction of unfolded segments in a protein sequence based on amino acid composition.

Coeytaux K, Poupon A.

Bioinformatics. 2005 May 1;21(9):1891-900.

PMID:
15657106
14.

BioRuby: bioinformatics software for the Ruby programming language.

Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T.

Bioinformatics. 2010 Oct 15;26(20):2617-9. doi: 10.1093/bioinformatics/btq475.

15.

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.

PMID:
15044236
16.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163.

17.

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.

18.

SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.

Wang CK, Broder U, Weeratunga SK, Gasser RB, Loukas A, Hofmann A.

Bioinformatics. 2012 Apr 1;28(7):1026-7. doi: 10.1093/bioinformatics/bts035.

PMID:
22332239
19.

Assessing the discordance of multiple sequence alignments.

Prakash A, Tompa M.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):542-51. doi: 10.1109/TCBB.2007.70271.

PMID:
19875854
20.

SPRINT: side-chain prediction inference toolbox for multistate protein design.

Fromer M, Yanover C, Harel A, Shachar O, Weiss Y, Linial M.

Bioinformatics. 2010 Oct 1;26(19):2466-7. doi: 10.1093/bioinformatics/btq445.

PMID:
20685957

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