Hi every body… I want to use haddock server- easy interface and I don’t have the active residue for filling the “Restraint definition” as part of easy interface because I don’t have any experimental data of the interface … but I want to know about active site before docking.
What is your suggestion about this?
Hi there,
If you do not have any experimental data of your own on the interface, there are several ways to ‘drive’ your docking, in decreasing order of reliability:
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Homology: You can search the PDB databank for structures of complexes whose proteins are homologous (high sequence similarity) to yours. Alternatively, you can look for structural homologs. Using these complexes and a sequence alignment between your protein and its homolog you can get a pretty good idea of an interface.
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Bioinformatics Predictions: You can use CPORT (better use the Prediction Interface of HADDOCK) or any other bioinformatics prediction tool to find patches on the surface of your proteins that are likely to be an interface.
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Center of Mass Restraints: This will just add a restraint to pull the two proteins together, without any particular bias. You cannot do this with the Easy interface. It also gives quite low-confidence results.
Alternatively, you can search in Pubmed for articles pinpointing important residues for your complex. Mutagenesis, truncation experiments, and others often help characterizing the interface of a complex without necessarily producing a structure.