The following services are available for modelling.
- Help with AlphaFold2
AlphaFold2 predicts a protein’s three-dimensional (3D) structure from its amino-acid sequence using an Artificial Intelligence (AI) system developed by DeepMind. We provide help and instructions how to run AlphaFold2 to predict the structure of your protein and its interactions with other proteins. Also, how to use AlphaFold2 to design constructs for protein expression.
- Structure-Function Studies
Inspection of the structure (experimental or predicted) and structure-based comparisons with other structures in the Protein Data Bank (PDB) for functional features and design of experiments.
- Homology Modelling
Using provided sequences, a search is carried out to identify homologous proteins with known structure in the PDB. The structures are then used as templates for homology modelling. In addition, if no structures are present in the PDB, ab initio calculations are carried out to identify the potential fold of the unknown protein. The use of AlphaFold2 is highly recommended.
- Protein-Ligand Docking
Ligands are docked into known structures to provide information about ligand-binding modes and the structural basis of ligand-binding affinities.
- Design of Mutants
Based on structural information, the design of mutants is proposed for further functional studies and a better understanding of individual residues in the function of the protein.