BRAGI: Linking and visualization of database information in a 3D viewer and modeling tool

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 1291-1293

  Reichelt, Joachim ^a   Dieterich, Guido ^a   Kvesic, Marsel ^b   Schomburg, Dietmar ^b   Heinz, Dirk W ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; INFORMATION PROCESSING; MACROMOLECULE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SWISS-PROT; THREE DIMENSIONAL IMAGING;

EID: 16344375771     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti138     Document Type: Article

References (19)

1. Berman,H.M., Battistuz,T, Bhat,T.N., Bluhm,W.F., Bourne,P.E., Burkhardt,K., Feng,Z., Gilliland,G.L., Iype,L., Jain,S. et al. (2002) The Protein Data Bank. Biopolymers, 22, 2577-2637.
2. Bernstein,H.J. (2000) Recent changes to RasMol, recombining the variants. Trends Biochem. Sci., 25, 453-455.
3. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
4. DeLano,W.L. (2002) The PyMOL Molecular Graphics System DeLano Scientific, San Carlos, CA.
5. Desmet,J., De Maeyer,M. and Lasters,I. (1997) Theoretical and algorithmical optimization of the dead-end elimination theorem. Nature 359, 539-542.
6. Dieterich,G., Heinz,D.W. and Reichelt,J. (2004) Matching of PDB chain sequences to information in public databases. J. Integr. Bioinformatics, 0007,2004.
7. Fechteler,T., Dengler,U. and Schomburg,D. (1995) Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria. J. Mol. Biol., 253 114-131.
8. Heger,A. and Holm,L. (2000) Towards a covering set of protein family profiles. Prog. Biophys. Mol. Biol., 73, 321-337.
9. Huang,C.C., Couch,G.S., Pettersen,E.F. and Ferrin,T.E. (1996) Chimera: an extensible molecular modeling application constructed using standard components. Pac. Symp. Biocomput., 1, 724.
10. Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD - Visual Molecular Dynamics. J. Mol. Graphics, 14, 33-38.
11. Krieger,E., Nabuurs,S.B. and Vriend,G. (2003) Homology methods. Biochem. Anal., 44, 509-523.
12. Lessel,U. and Schomburg,D. (1999) Importance of anchor group positioning in protein loop prediction. Proteins, 37, 56-64.
13. McKusick-Nathans,V.A. (2000) Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, Online Mendelian Inheritance in Man, OMIM (TM).
14. O'Donoghue,S.I., Meyer,J.E., Schafferhans,A. and Fries,K. (2004) The SRS3D module: integrating structures, sequences, and features. Bioinformatics, 20, 2476-2478.
15. POV-Ray (1991-2002) Persistence of Vision™ Ray Tracer (POV-Ray™).
16. Schomburg,D. and Reichelt,J. (1988) BRAGI: a comprehensive protein modeling program system. J. Mol. Graphics, 6, 161-165.
17. Schwede, T., Kopp,J., Guex,N. and Peitsch,M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385.
18. Wohlfahrt,G., Hangoc,V. and Schomburg,D. (2002) Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements. Proteins, 47, 370-378.
19. Zdobnov,E.M. and Apweiler,R. (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.