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3DM: Protein engineering Super-family platforms Bio-Prodict 3DM super-family systems Henk-Jan Joosten Remko Kuipers Tom v/d Bergh Bas Vroling 2012-01-25 3DM: Protein engineering Super-family platforms Bio-Prodict Founded 2008 Spinoff WUR 4 Employees New office in Nijmegen 3DM: Protein engineering Super-family platforms 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 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: Protein engineering Super-family platforms + 3D Numbers -> structure – alignment link 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms Amino acid data Mutation data (literature, Swiss-Prot, OMIM, other mutation data bases) 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). Functional data (glycosilation, phosphorylation, active site, etc) SNP (SNP databases, genome sequencing projects) All data are stored connected to the 3D numbering scheme and thus to the alignment, to the structures and each other * For publication see: www.bio-prodict.nl 3DM: Protein engineering Super-family platforms * For publication see: www.bio-prodict.nl 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms 3DM: Protein engineering Super-family platforms Conclusion 3DM: Protein engineering Super-family platforms Conclusion 3DM: Protein engineering Super-family platforms Newprot Visibility New tools 3DM: Protein engineering Super-family platforms Thank you for your attention
