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•Dutch national centre for computational molecular sciences research

•Research groups –Comparative Genomics & Systems Biology (Huynen) –Bacterial Genomics (Siezen)–Computational Drug Design (De Vlieg)–Bioinformatics of Macromolecular Structures (Vriend)

•Training & Education –BSc, MSc, PhD and PostDoc programmes –International workshops–Hotel Bioinformatica–High school courses

•Computational facilities, databases, and software packages via (inter-)national service platforms (NBIC, EBI, etc)

•NBIC: National BioInformatics Centre.

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CMBI - Centre for Molecular and Biomolecular Informatics

Bioinformatics @CMBI

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Computational Drug Discovery (CDD) Group

• Head: Prof. Jacob de Vlieg

• Key Research Fields– Structural bioinformatics for drug design– Bioinformatics for genomics (microarray analysis, text mining, etc)– Translational medicine informatics

Academic ResearchNew scientific approachesTraining & education

ApplicationsExciting real life problems

‘wet’ validationCDD

Bridging academic research and applied genomics

Bioinformatics @CMBI

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Bacterial Genomics Group

• Head: Prof Roland Siezen

• Research interest: Biological questions in the interest of Dutch Food Industry

• How can we improve:– fermentation – safety – health

• Micro-organisms studied: Gram-positive food bacteria:– lactic acid bacteria (Lactococcus, Lactobacillus)– spoilage bacteria (Listeria, Clostridium, Bacillus cereus)

listeria

lactococcus

Bioinformatics @CMBI

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Comparative Genomics Group

• Head: Prof. Martijn Huynen

• Research Focus: – How do the proteins encoded in genomes interact with each other to

produce cells and phenotypes ? – To predict such functional interactions between proteins as there exist

e.g. in metabolic pathways, signalling pathways or protein complexes

Which genes do two genomes share (and which genes do they not share) and can we relate this to their phenotype?

Bioinformatics @CMBI

Comparative genomics

Prediction of protein function, pathways

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Bioinformatics of macromolecular structures

•Head: Prof. Gert Vriend

•Research Focus: Understanding proteins (and their environment)

•Proteins are the core of life, they do all the work, and they give you feelings, contact with the outside world, etc.

•Topics:– Homology modeling technology and applications– Protein engineering– Application of bioinformatics in medical research (Hanka Venselaar)– Structure validation and structure determination improvement– Molecular class specific information systems (e.g. GPCRDB & NucleaRDB)– Data mining– WHAT IF molecular modelling and visualization software

Bioinformatics @CMBI

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The three mutated residues are all important for the correct positioning of Tyrosine 111Tyrosine 111 is important for substrate binding

Ahmed et al., Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans. Nat Genet. 2008 Nov;40(11):1335-40.

Homology Modeling

Bioinformatics @CMBI

Interested? Contact Hanka Venselaar (h.venselaar@cmbi.ru.nl)Project HOPE: Have yOur Protein Explained

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Human genome, great expectations

Data ≠ Knowledge, insight !!!

Bioinformatics