3dm: protein engineering super-family platforms bio-prodict 2012-01-25 3dm super-family systems...

3DM: Protein engineering Super-family platforms

Bio-Prodict

2012-01-25

3DM super-family systems

Henk-Jan JoostenRemko KuipersTom v/d Bergh

Bas Vroling

3DM: Protein engineering Super-family platforms

Bio-Prodict

Founded 2008 Spinoff WUR 4 Employees New office in Nijmegen

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

3DM: Protein engineering Super-family platforms

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3D Numbers -> structure – alignment link

3DM: Protein engineering Super-family platforms

3DM: Protein engineering Super-family platforms

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)

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

VisibilityNew tools

3DM: Protein engineering Super-family platforms

Thank you for your attention