Sir,
here i have 1 query what do you mean by cluster.
what signifies about cluster 1_4 and 6_4 is there any difference if it is then what is that.
how can we defend our best pose and docking score
which one will be our most appropriate dock pose
is there any significance due to number present in 1_4 and 6_4
it will help me on my research and also in analysis of my results
Cluster 1 (what signifies all these values)
HADDOCK score -191.3 +/- 3.2
Cluster size 81
RMSD from the overall lowest-energy structure 6.3 +/- 0.1
Van der Waals energy -66.3 +/- 7.2
Electrostatic energy -446.1 +/- 42.9
Desolvation energy -60.2 +/- 6.8
Restraints violation energy 244.9 +/- 20.15
Buried Surface Area 1874.0 +/- 68.8
Z-Score -1.8
Another question is like what do you men by Nr 1 best structure how can we defend that
Nr 1 best structure Download structure
Nr 2 best structure Download structure
Nr 3 best structure Download structure
Nr 4 best structure Download structure
The cluster first number indicates the size of the cluster, i.e. cluster1_… is the largest cluster.
The second number indicated the rank of a given model within that cluster, i.e. cluster1_4 is model #4 from cluster1
The cluster ranking is however given by the HADDOCK score.
It sounds like some reading would be best… especially if you have no idea what some of those terms mean.
Start with the basic JACS 2003 HADDOCK paper. Have a look at our server papers Nature Protocols 2010 and JMB.
- C. Dominguez, R. Boelens and A.M.J.J. Bonvin HADDOCK:
A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737 (2003).
You can find info on the HADDOCK software web page and manual at:
http://www.bonvinlab.org/software/haddock2.2/
http://www.bonvinlab.org/software/haddock2.2/manual/
And specific about scoring:
http://www.bonvinlab.org/software/haddock2.2/scoring/
Also check our Methods in Molecular Biology papers describing the use of HADDOCK, e.g.:
-
C. Geng, S. Narasimhan, J. P.G.L.M. Rodrigues and A.M.J.J. Bonvin. Information-driven,
ensemble flexible peptide docking using HADDOCK.Methods in Molecular Biology: Modeling Peptide-Protein Interactions. Eds Ora Schueler-Furman and Nir London. Humana Press Inc. 1561 ,
109-138 (2017). -
M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. Information-driven
modelling of protein-peptide complexes. Methods in Molecular Biology. Ed. Peng Zhou. Humana Press Inc. 221-239 (2015) -
J.P.G.L.M Rodrigues, E. Karaca and A.M.J.J. Bonvin. Information-driven
structural modelling of protein-protein interactions. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 399-424 (2015). -
G.C.P. van Zundert and A.M.J.J. Bonvin. Modeling
protein-protein complexes using the HADDOCK webserver. Methods in Molecular Biology: Protein Structure Prediction. Ed. Daisuke Kihara. Humana Press Inc., 163-179 (2014).
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