Question: How To Calculate The Contribution Of Interacting Amino Acids In Binding
3
gravatar for Hari
7.7 years ago by
Hari250
Hari250 wrote:

Hi all, I would like to know how to calculate the contribution of residues towards binding especially the interacting residues in a known (pdb) protein complex.I did look at the servers suggested for this question http://biostar.stackexchange.com/questions/8354/important-residues-for-protein-protein-binding However i would like to know if there are other servers or methods that can do this.For.ex one parameter that would give the contribution of these interacting amino acids would be the interaction energy.Can i calculate this without having to do docking or simuation?

Thanks in advance for your suggestions.

ADD COMMENTlink modified 7.7 years ago by Dkoes10 • written 7.7 years ago by Hari250

Is a tertiary structure of the complex available?

ADD REPLYlink written 7.7 years ago by Jan Kosinski1.6k

yes it is for known structures.

ADD REPLYlink written 7.7 years ago by Hari250

3d structure is available,i have edited the question accordingly

ADD REPLYlink written 7.7 years ago by Hari250

Both Robetta server and Anchor are quite useful for predicting hot-spots,one is accepted answer but +1 for both the answers,thanks a lot

ADD REPLYlink written 7.7 years ago by Hari250
4
gravatar for Jan Kosinski
7.7 years ago by
Jan Kosinski1.6k
Jan Kosinski1.6k wrote:

Perform so called computational alanine scanning and prediction of hot spot residues.

Although you must refer to the recent literature for the currently best methods and their performances, I can suggest you some to start:

ADD COMMENTlink written 7.7 years ago by Jan Kosinski1.6k

Thanks for the suggestions

ADD REPLYlink written 7.7 years ago by Hari250
1
gravatar for Dkoes
7.7 years ago by
Dkoes10
University of Pittsburgh
Dkoes10 wrote:

PocketQuery is the successor of ANCHOR. It has pre-calculated delta G (from FastContact, like ANCHOR) and delta delta G (from Rosetta) values for all the PPIs in the PDB. You can also submit your own structure, although this takes longer to process than ANCHOR due to the Rosetta and sequence conservation calculations.

PocketQuery is designed to support the identification of small-molecule inhibitor starting points, so it performs an analysis on all possible clusters of co-located residues and allows you to output the result to various pharmacophore search engines. However, by setting the cluster size to 1 and setting the view to Residue Centric you can explore the PPI interface at a per residue level. Also, the viewer controls allow you to color interface residues based on their properties.

ADD COMMENTlink written 7.7 years ago by Dkoes10

+1 for the suggestions

ADD REPLYlink written 7.7 years ago by Hari250
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