CCL: apo enzyme
- From: "Elaine Meng" <meng^cgl.ucsf.edu>
- Subject: CCL: apo enzyme
- Date: Thu, 28 Aug 2008 14:03:48 -0400
Sent to CCL by: "Elaine Meng" [meng^cgl.ucsf.edu]
This isn't my main area of work nowadays, so I don't know of a good review off
the top of my head.
However, I tried searching PubMed using
("binding site"[tiab] OR "active site"[tiab]) AND
prediction[tiab] AND review[pt]
which yielded some possibly useful articles including
Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA.
Free resources to assist structure-based virtual ligand screening experiments.
Curr Protein Pept Sci. 2007 Aug;8(4):381-411. Review.
Laurie AT, Jackson RM.
Methods for the prediction of protein-ligand binding sites for structure-based
drug design and virtual ligand screening.
Curr Protein Pept Sci. 2006 Oct;7(5):395-406. Review.
Receptor-binding sites: bioinformatic approaches.
Methods Mol Biol. 2006;316:291-358. Review.
Also, publications describing the many various individual methods usually
include some estimate of success rate based on comparison to a set of knowns,
sometimes relative to other similar methods. I remember the CASTp papers saying
that in some high percentage of cases, the largest pocket is the active or
binding site of a protein.
Elaine C. Meng, Ph.D. meng*_*cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco