| Superfamily member |
Links to programs that generate information useful for COMPARER in deriving structure-based sequence alignment |
ATM2SEQ, SEQ
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Generate sequence file in PIR format from the PDB file |
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SSTRUC, SST
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Produce the secondary structure information from PDB |
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PSA, PSA
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Generate solvent accessible information from the PDB file |
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HBOND, HBD
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Produce hydrogen bonding patterns between mainchain–mainchain and mainchain–sidechain of the protein |
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For each PDB entry within the superfamily, there are various links with other database entries |
RCSB |
Research Collaboratory for Structural Bioinformatics—PDB |
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EBI |
European Bioinformatics Institute |
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SCOP |
Structural Classification of Proteins |
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HOMSTRAD |
Homologous Structure Alignment Database |
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DDBASE |
Dial-Derived Domain Database |
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CATH |
Class Architecture Topology and Homologous superfamily |
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FSSP |
Fold classification based on Structure–Structure alignment of Proteins |
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DSDBASE |
Disulphide Database |
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PALI |
Phylogeny and Alignment of homologous protein structures |
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PRESAGE |
Collaborative resource for structural genomics |
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MODBASE |
A database of annotated comparative protein structure models |
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3Dee |
A database of protein domain definitions |
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PQS |
Protein Quaternary Structure query form at the EBI |
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STING |
Tool for the simultaneous display of information about macromolecule structure and sequence |
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GRASS |
Graphical Representation and Analysis of Structure Server |
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LPC/CSU |
Ligand–Protein Contacts and Contacts of Structural |
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LPFC |
Library of Protein Family Cores |
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MMDB |
Molecular Modelling DataBase, NCBI |
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GeneCensus |
GeneCensus genome comparisons |
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SYSTERS |
Classification of sequences from SWISS-PROT and PIR into disjoint family clusters and hierarchically into superfamily and subfamily clusters |
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CE |
Databases and tools for 3D protein structure comparison and alignment |
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PROMOTIF |
PROMOTIF v.1.0 for analysing protein structural motifs |
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PROCHECK |
Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry |
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PDBSUM |
Summaries and structural analyses of PDB data files |
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Pfam |
Protein families database of alignments and HMMs |
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WHATCHECK |
WHAT-CHECK: free WHAT IF verification subset |
