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