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Items: 1 to 20 of 339

1.

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.

2.

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.

3.

Defining 3D residue environment in protein structures using SCORPION and FORMIGA.

Higa RH, Oliveira AG, Horita LG, Miura RT, Inoue MK, Kuser PR, Mancini AL, Yamagishi ME, Togawa RC, Neshich G.

Bioinformatics. 2004 Aug 12;20(12):1989-91. Epub 2004 Mar 25.

4.

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.

Neshich G, Rocchia W, Mancini AL, Yamagishi ME, Kuser PR, Fileto R, Baudet C, Pinto IP, Montagner AJ, Palandrani JF, Krauchenco JN, Torres RC, Souza S, Togawa RC, Higa RH.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W595-601.

5.

STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces.

Mancini AL, Higa RH, Oliveira A, Dominiquini F, Kuser PR, Yamagishi ME, Togawa RC, Neshich G.

Bioinformatics. 2004 Sep 1;20(13):2145-7. Epub 2004 Apr 8.

6.

The Star STING server: a multiplatform environment for protein structure analysis.

Neshich G, Mazoni I, Oliveira SR, Yamagishi ME, Kuser-Falcão PR, Borro LC, Morita DU, Souza KR, Almeida GV, Rodrigues DN, Jardine JG, Togawa RC, Mancini AL, Higa RH, Cruz SA, Vieira FD, Santos EH, Melo RC, Santoro MM.

Genet Mol Res. 2006 Dec 1;5(4):717-22.

7.

The Diamond STING server.

Neshich G, Borro LC, Higa RH, Kuser PR, Yamagishi ME, Franco EH, Krauchenco JN, Fileto R, Ribeiro AA, Bezerra GB, Velludo TM, Jimenez TS, Furukawa N, Teshima H, Kitajima K, Bava A, Sarai A, Togawa RC, Mancini AL.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W29-35.

8.

PDB-Metrics: a web tool for exploring the PDB contents.

Fileto R, Kuser PR, Yamagishi ME, Ribeiro AA, Quinalia TG, Franco EH, Mancini AL, Higa RH, Oliveira SR, Santos EH, Vieira FD, Mazoni I, Cruz SA, Neshich G.

Genet Mol Res. 2006 Jun 30;5(2):333-41.

9.

STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database.

Neshich G, Mancini AL, Yamagishi ME, Kuser PR, Fileto R, Pinto IP, Palandrani JF, Krauchenco JN, Baudet C, Montagner AJ, Higa RH.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D269-74.

10.

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes.

Higa RH, Togawa RC, Montagner AJ, Palandrani JC, Okimoto IK, Kuser PR, Yamagishi ME, Mancini AL, Neshich G.

BMC Bioinformatics. 2004 Aug 9;5:107.

11.

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.

12.

VISTAL--a new 2D visualization tool of protein 3D structural alignments.

Kolodny R, Honig B.

Bioinformatics. 2006 Sep 1;22(17):2166-7. Epub 2006 Jul 12.

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.

14.

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling.

Arnold K, Bordoli L, Kopp J, Schwede T.

Bioinformatics. 2006 Jan 15;22(2):195-201. Epub 2005 Nov 13.

15.

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.

16.

A web-based three-dimensional protein retrieval system by matching visual similarity.

Yeh JS, Chen DY, Chen BY, Ouhyoung M.

Bioinformatics. 2005 Jul 1;21(13):3056-7. Epub 2005 Apr 19.

17.

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W416-9. Epub 2007 May 8.

18.

Tools for integrated sequence-structure analysis with UCSF Chimera.

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE.

BMC Bioinformatics. 2006 Jul 12;7:339.

19.
20.

BSDD: Biomolecules Segment Display Device--a web-based interactive display tool.

Selvarani P, Shanthi V, Rajesh CK, Saravanan S, Sekar K.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W645-8.

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