CCL: Characterization of binding pocket (hydrophobic or hydrophilic) ?

 Sent to CCL by: Julien Lefeuvre [j.lefeuvre\a/iecb.u-bordeaux.fr]
 Tiejun Cheng tjcheng^-^mail.sioc.ac.cn wrote:
 > Sent to CCL by: "Tiejun  Cheng" [tjcheng::mail.sioc.ac.cn]
 > Dear CCLers,
 >
 > Is there any methods or softwares that can determine whether a binding
 pocket is hydrophobic or hydrophilic? Thanks in advance.
 >
 > Best regards,
 >
 > Jay
 Hi Jay,
 I am not sure if it will fit your needs, but I wrote "pymlp" to
 calculate lipophilicity potential maps of protein for vmd and pymol.
 Pymlp is a refurbished version of some former fortran code called MLPP.
 You may found it here:
 http://code.google.com/p/pymlp/
 The code is a bit slow right now and I have some much faster code in
 house ... but it needs more time before release.
 =============================
 pyMLP: Molecular Lipophilicity Potential evaluator
 pyMLP is a program computing the molecular lipophilicity
 potential map of proteins.
 --------------------------------------------------------------------------------
 Please include this reference in published work using pyMLP:
 Broto P., Moreau G., Vandycke C. -
 `Molecular structures: Perception, autocorrelation descriptor and sar
 studies.
  System of atomic contributions for the calculation of the n-octanol/water
  partition coefficients', Eu. J. Med. Chem. 1984, 19.1, 71-78
 Laguerre M., Saux M., Dubost J.P., Carpy A. -
 `MLPP: A program for the calculation of molecular lipophilicity potential in
  proteins', Pharm. Sci. 1997, 3.5-6, 217-222
 --------------------------------------------------------------------------------
 This program was developed in python as a platform independent
 equivalent of MLPP (see references). As a result pyMLP may run on any
 platform supported by Python and Numpy.
 =============================
 HIH
 Julien Lefeuvre