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Items: 1 to 20 of 112


InterMap3D: predicting and visualizing co-evolving protein residues.

Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG.

Bioinformatics. 2009 Aug 1;25(15):1963-5. doi: 10.1093/bioinformatics/btp335. Epub 2009 Jun 15.


MatrixPlot: visualizing sequence constraints.

Gorodkin J, Staerfeldt HH, Lund O, Brunak S.

Bioinformatics. 1999 Sep;15(9):769-70.


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.


Using information theory to search for co-evolving residues in proteins.

Martin LC, Gloor GB, Dunn SD, Wahl LM.

Bioinformatics. 2005 Nov 15;21(22):4116-24. Epub 2005 Sep 13.


FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB.

Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Mølgaard A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W84-8.


PAR-3D: a server to predict protein active site residues.

Goyal K, Mohanty D, Mande SC.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W503-5. Epub 2007 May 3.


PROCAIN server for remote protein sequence similarity search.

Wang Y, Sadreyev RI, Grishin NV.

Bioinformatics. 2009 Aug 15;25(16):2076-7. doi: 10.1093/bioinformatics/btp346. Epub 2009 Jun 3.


BioShell--a package of tools for structural biology computations.

Gront D, Kolinski A.

Bioinformatics. 2006 Mar 1;22(5):621-2. Epub 2006 Jan 10.


3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.

Bennett SP, Nevill-Manning CG, Brutlag DL.

Bioinformatics. 2003 Mar 1;19(4):541-2.


The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries.

Fischer D, Paś J, Rychlewski L.

Bioinformatics. 2004 Oct 12;20(15):2482-4. Epub 2004 Apr 8.


QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.

Suhrer SJ, Gruber M, Sippl MJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W411-5. Epub 2007 May 3.


Mapping PDB chains to UniProtKB entries.

Martin AC.

Bioinformatics. 2005 Dec 1;21(23):4297-301. Epub 2005 Sep 27.


DOMAC: an accurate, hybrid protein domain prediction server.

Cheng J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W354-6. Epub 2007 Jun 6.


Template-based and free modeling by RAPTOR++ in CASP8.

Xu J, Peng J, Zhao F.

Proteins. 2009;77 Suppl 9:133-7. doi: 10.1002/prot.22567.


AQUA: automated quality improvement for multiple sequence alignments.

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P.

Bioinformatics. 2010 Jan 15;26(2):263-5. doi: 10.1093/bioinformatics/btp651. Epub 2009 Nov 19.


PROFbval: predict flexible and rigid residues in proteins.

Schlessinger A, Yachdav G, Rost B.

Bioinformatics. 2006 Apr 1;22(7):891-3. Epub 2006 Feb 2.


ENDscript: a workflow to display sequence and structure information.

Gouet P, Courcelle E.

Bioinformatics. 2002 May;18(5):767-8.


Domain-based small molecule binding site annotation.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, Hogue CW.

BMC Bioinformatics. 2006 Mar 17;7:152.


OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.


MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields.

Xia X, Zhang S, Su Y, Sun Z.

Bioinformatics. 2009 Jun 1;25(11):1433-4. doi: 10.1093/bioinformatics/btp251. Epub 2009 Apr 9.

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