Peptide docking and design

AlgoModel includes a module for flexible peptide docking to targets. The docking module allows peptide docking with:

• full main chain and side chain flexibility of the peptide
• translational & rotational freedom
• neighbouring protein side chains treated as flexible
  

The docking methodology of AlgoModel is:

• Robust: several test sets can be docked with one scoring function
• Transferable: the scoring function applies to several receptors - ligand systems
• Validated in various protein/peptide complexes

Loop building

• The loop-builder module in AlgoModel allows de novo loop modeling, which is especially of interest for the design and modelling of therapeutic antibodies.
• AlgoModel is used for loop rearrangements upon ligand binding as well as loop maturation, evaluating the stability of a given loop and optimizing the loop.
• The loop generator is built on full atom energy calculations using combined main chain/side chain rotamers. It performs substantially better compared to other commercially available programs.