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

 Sent to CCL by: Dr David N Haney [haney-$-edusoft-lc.com]
 Dear Jay,
 I just sent a post about hydrophobicity under the subject
 "calculating and displaying surface residues".   Binding pockets are
 surface residues, and HINT is one of the best tools for displaying the
 hydropathic (hydrophobic/hydrophilic) nature as well as calculating the
 components of the hydropathic "energies".  For a ligand bound to the
 binding
 pocket, you can determine the relative contributions of the hydrophobic and
 hydrophilic parts.
 ####
 > Although HINT is not freeware, it is one of the best tools to display
 > hydrophobic energy surfaces as well as hydrophobic-hydrophobic surface
 interactions.
 > HINT scoring has been shown to provide a good correlation with binding
 energy.
 > It is currently available as a TOOLKIT and the libraries can be used with
 > external programs like PyMol.
 >
 > Please see www.edusoft-lc.com/hint ++
 > J. Med. Chem. 1991, 34, 758-767.
 > J. Computer Aided Mol. Design 1991, 5, 545-552.
 > J. Med. Chem. 2003, 46, 4487-4500.
 > J. Med. Chem. 2004, 47, 4507-4516.
 > J. Mol. Biol. 2006, 358, 289–309
 ####
 On Wed, Mar 12, 2008 at 09:45:43AM -0400, 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>
 --
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