When looking for diversity in protein structures, the volume-based or the shape-based analysis of a binding side through SiteMap is more meaningful than looking at the RMSD metric alone, as mentioned in a recent protein preparation Schrodinger webinar by Dr Woody Sherman, which can be found here:
http://www.schrodinger.com/seminarprior/19/38/
To evaluate protein structure diversity with SiteMap you can perform the following steps:
1. Run SiteMap on each structure -- Computes shape of binding pocket for each structure
3.Generate pairwise volume overlap matrix with the Python script from Script Center "trajectory_binding_site_volumes.py"
4.Perform hierarchical clustering to get diverse binding sites with "volume_cluster.py"
5. Choose desired structures
See also:
Halgren T (2007) Chem Biol Drug Des 69(2):146 title: "New method for fast and accurate binding-site identification and analysis."
Halgren T (2009) J Chem Inf Model 49:377 title: "Identifying and characterizing binding sites and assessing druggability."
Eva
http://www.schrodinger.com/seminarprior/19/38/
To evaluate protein structure diversity with SiteMap you can perform the following steps:
1. Run SiteMap on each structure -- Computes shape of binding pocket for each structure
3.Generate pairwise volume overlap matrix with the Python script from Script Center "trajectory_binding_site_volumes.py"
4.Perform hierarchical clustering to get diverse binding sites with "volume_cluster.py"
5. Choose desired structures
See also:
Halgren T (2007) Chem Biol Drug Des 69(2):146 title: "New method for fast and accurate binding-site identification and analysis."
Halgren T (2009) J Chem Inf Model 49:377 title: "Identifying and characterizing binding sites and assessing druggability."
Eva
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