Protein Modelling Methods used by ProMod

Method:

Knowledge-based approach.

Requirements:

• At least one known 3D-structure of a related protein.
• Good quality sequence alignements; the reliability of the model is determined by the degree of sequence identity.

Procedures:

• Superposition of related 3D-structures.
• Generation of a multiple a alignement with the sequence to be modelled.
• Generation of a Framework for the new sequence.
• Rebuild lacking Loops.
• Complete and correct BackBone.
• Correct and rebuild Side Chains.
• Verify model structure quality and check Packing.
• Refine structure by Energy minimisation and Molecular Dynamics.