PDBpaint, a visualization webservice to tag protein structures with sequence annotations

Bioinformatics

Volumn 27, Issue 18, 2011, Pages 2605-2606

  Fournier, David ^a   Andrade Navarro, Miguel A ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; INTERNET; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

AMINO ACIDS; INTERNET; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 80052783523     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr419     Document Type: Article

References (21)

1. Ashkenazy,H. et al. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res., 38, W529-W533.
2. Emanuelsson,O. et al. (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc., 2, 953-971.
3. Finn,R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
4. Gaulton,A. and Attwood,T.K. (2003) Motif3D: relating protein sequence motifs to 3D structure. Nucleic Acids Res., 31, 3333-3336.
5. Holm,L. and Rosenstrom,P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38, W545-W549.
6. Jmol (2011) Jmol: an open-source Java viewer for chemical structures in 3D. Available at: http://www.jmol.org/.
7. Krogh,A. et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
8. Liu,Z.P. et al. (2008) Bridging protein local structures and protein functions. Amino Acids, 35, 627-650.
9. Magrane,M. and Consortium,U. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database, 2011 [Epub ahead of print, doi:10.1093/database/bar009].
10. Murzin,A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
11. O'Donoghue,S.I. et al. (2004) The SRS 3D module: integrating structures, sequences and features. Bioinformatics, 20, 2476-2478.
12. O'Donoghue,S.I. et al. (2010) Visualization of macromolecular structures. Nat. Methods, 7, S42-S55.
13. Palidwor,G.A. et al. (2009) Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput. Biol., 5, e1000304.
14. Pettifer,S.R. et al. (2004) UTOPIA-User-Friendly Tools for Operating Informatics Applications. Comp. Funct. Genomics, 5, 56-60.
15. Pieper,U. et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res., 39, D465-D474.
16. Rose,P.W. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
17. Roy,A. et al. (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.
18. Saqi,M.A. and Sayle,R. (1994) PdbMotif-a tool for the automatic identification and display of motifs in protein structures. Comput. Appl. Biosci., 10, 545-546.
19. Sayle,R. and Bissell,A. (1992) RasMol: a program for fast realistic rendering of molecular structures with shadows. In Proceedings of the 10th Eurographics UK 92 Conference, University of Edinburgh, UK.
20. Soding,J. et al. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
21. Zhang,Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40.