Links and Supplements
References
[
Structural Bioinformatics |
Perl for Bioinformatics |
2010 Nucleic Acids Research Data Base Issue
]
Data Bases and Web Servers
[
PDB |
MMDB |
SCOP |
CATH |
DALI/FSSP |
3Dee |
VAST |
DOMAC |
Domain Parser |
pDomains |
PRODOM |
PFAM |
CDD |
PROSITE |
DOMPRED |
PISCES |
I-SITES
]
Viewers and Tutorials on Visualization
[
Swiss PDB Viewer |
Jmol |
Rasmol |
Molscript |
Protein Explorer |
TOPS |
RASMOL Quick reference |
Eric Martz' webpage (MolviZ/Jmol) |
Gale Rhodes' DeepView tutorial |
Gale Rhodes' RasMol tutorial
]
Bioinformatics Links
[
ZLAB from Boston University |
Bioinformatics Tools for Protein Structures
]
Info on Structure, Motif, Domain
[
PDF file format |
Principles of Protein Structure |
Terminolgy: Motif, Fold, Domain |
Key for I-SITES profiles
]
Wikipedia
[
Protein Structure |
Protein Domain
]
References
Alexandrov and Shindyalov (2003): PDP: protein domain parser.
Andreeva et al (2004): SCOP database in 2004: refinements integrate structure and sequence family data.
Bateman et al (2004): The Pfam protein families database.
Berman et al (2000): The Protein Data Bank.
Holm and Sander (1993): Protein structure comparison by alignment of distance matrices.
Holm and Sander (1994): The FSSP database of structurally aligned protein fold families.
Holm and Sander (1996): Mapping the protein universe.
Holm and Sander (1998): Touring protein fold space with Dali/FSSP.
Murzin et al (1995): SCOP: a structural classification of proteins database for the investigation of sequences and structures.
Novotny and Kleywegt (2005): survey of left-handed helices in protein structures.
Orengo et al (1997): CATH - a hierarchic classification of protein domain structures.
Pearl et al (2005): The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Thornton et al (1999): Protein folds, functions and evolution.