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3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DMProtein super-family data integration
Tom van den Bergh
Bio-Prodict
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
Superimposing family structures69 P450 structures
These structures are sequentially all different: <80%
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
Structure based alignments
Structural conserved residues get the same 3D- number because
these residues have a similar role in the
proteins
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3D number: the alignment structure link
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
Amino acid data
• Mutation dataliterature, Swiss-Prot, OMIM, …> 25.000 mutations searchable for effects!!!!
• Structure dataPPI, ligand contacts, bridges, solvent accessibility, flexibility/RMSD, …
• Alignment dataConservation, correlated mutations, family specific residues, …
• SNP dataSNP databases, genome sequencing projects
• Data integrationAll data are stored connected to the 3D numbering scheme and thus to the alignment, to the structures and each other
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms
3DM: Protein Super-family Platforms3DM: Protein Super-family Platforms