
Ulrike Uhrig
Computational Chemistry
Computational chemistry methods are integral to the process of active molecule identification and optimisation. These include:
- Chemoinformatics approaches
- Molecular modelling
- Computational screening using ligand-based and structure-based design strategies
- Managing compound acquisition through our chemistry partners
- Commercial software available: SYBYL-X including SurflexDock and SurflexSim, LeadIT including FlexX and FlexS, Muse, Spartan
- Access to the HPC compute cluster at EMBL which provides access to more than 5800 CPUs for scientific computing at EMBL
Structural biology
- Protein structure visualisation (3D visualisation capabilities)
- Binding site identification
- Analysis of interaction profiles of ligands inside a binding site
- Homology modeling; leveraging known protein structures to unknowns with similar sequence
Ligand-based design
- Pharmacophore elucidation based on known active ligands
- Database searching for new active compounds based on pharmacophore
- Properties prediction based on models from data of known ligands
- SAR, ADME predictions based on data from known ligands
Receptor-based design
- Docking of ligands into target structure
- Virtual screening; selection of compounds from large data set based on docking
- Ligand refinement based on docked structure
- De novo design of ligands from protein structure; no lead compound; spatial arrangement of suitable binding groups
Library design
- Diversity and similarity tools
- Library creation
- For random screening
- For specific targets
- Exploration of SAR (iterative)

Data analysis approaches
Data analysis
- Analysis of screening data; clustering hit compounds and prioritisation for follow-up investigations
Compound acquisitions
- Identifying vendors and availability of desired compounds
- Quote requests