1. 3DM: Protein engineering Super-family platforms Bio-Prodict 2012-01-25 3DM super-family systems Henk-Jan Joosten Remko Kuipers Tom v/d Bergh Bas Vroling

2. 3DM: Protein engineering Super-family platforms Bio-Prodict Founded 2008 Spinoff WUR 4 Employees New office in Nijmegen

3. 3DM: Protein engineering Super-family platforms Enzyme Engineering: Changing specificity and activity, inhibitor design, increasing thermostability and enantio selectivity. DNA diagnostics: pathogenicity prediction of DNA variants Drug design: inhibitor design, ligand binding analysis, discrimination agonist/antagonist 3DM: Systematic analysis of heterogeneous super-family data to discover protein functionalities Connect different data types: Structures, sequences, mutations, annotations, correlations, contacts, etc Data visualization: Online, In structures, In articles

4. 3DM: Protein engineering Super-family platforms + 3D Numbers -> structure – alignment link

5. 3DM: Protein engineering Super-family platforms

6. Mutation data (literature, Swiss-Prot, OMIM, other mutation data bases) * For publication see: www.bio-prodict.nl Amino acid data All data are stored connected to the 3D numbering scheme and thus to the alignment, to the structures and each other Data from PDB files (protein-protein interactions, ligand contacts, bridges, solvent accessibility, flexibility/RMSD, etc) Alignment data (correlated mutations, conservation, family specific residues, residue abundance, etc). SNP (SNP databases, genome sequencing projects) Functional data (glycosilation, phosphorylation, active site, etc)

7. 3DM: Protein engineering Super-family platforms * For publication see: www.bio-prodict.nl

8. 3DM: Protein engineering Super-family platforms

14. Conclusion

15. 3DM: Protein engineering Super-family platforms Conclusion

16. 3DM: Protein engineering Super-family platforms Newprot Visibility New tools

17. 3DM: Protein engineering Super-family platforms Thank you for your attention