[Chimera-users] surface hydrophobicity display

Sumitro Harjanto sharjanto at i2r.a-star.edu.sg
Mon Jan 31 21:46:04 PST 2011

Hi Elaine and Tom,

Thanks for going the extra mile to come up with such a comprehensive
reply. This is a lot of info to digest and softwares to explore. Will
try them out. Thanks! =]


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, February 01, 2011 11:29 AM
To: Sumitro Harjanto
Cc: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] surface hydrophobicity display

One more: the program "hint" (Hydropathic INTeractions).  It's
embarrassing that I  forgot to mention this, since I've actually used
the program for DOCK scoring and published the results, which were
pretty good. It is not free, however.

Here is the hint website:

It comes as a module to other packages such as SYBYL, or as a
standalone.  I don't know if the standalone includes the option to
output 3D maps.

On Jan 31, 2011, at 9:55 AM, Elaine Meng wrote:

> Hi Sumitro,
> I did a little more digging for related information and thought I
would share -- however, none of these methods are available in Chimera
> Miguel Ortiz Lombardia has pointed out that the GRID program
calculates a hydrophobic potential, and sent us the following links:
> <http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html>
> <http://www.moldiscovery.com/docs/vsplus/grid.html>
> -- the following web server sounded promising, but apparently no
longer exists:
> PLATINUM: a web tool for analysis of hydrophobic/hydrophilic
organization of biomolecular complexes.
> Pyrkov TV, Chugunov AO, Krylov NA, Nolde DE, Efremov RG.
> Bioinformatics. 2009 May 1;25(9):1201-2.
> <http://www.ncbi.nlm.nih.gov/pubmed/19244385>
> -- the following paper discusses what surface properties of the
receptor correlate well with the types of nearby ligand atoms.  If I
understood it correctly, they looked at how successfully Coulombic
electrostatic potential and the gradient in that potential can be used
to identify hydrophobic areas of surface (areas that bind hydrophobic
atoms in the ligand).  Both were somewhat successful, but even better
was a simple definition of hydrophobic surface as the part of the
surface that is not close to hydrogen-bonding groups.  This paper is
fairly old and the data set of ligand/receptor structures small.
> Definition and display of steric, hydrophobic, and hydrogen-bonding
properties of ligand binding sites in proteins using Lee and Richards
accessible surface: validation of a high-resolution graphical tool for
drug design.
> Bohacek RS, McMartin C.
> J Med Chem. 1992 May 15;35(10):1671-84.
> <http://www.ncbi.nlm.nih.gov/pubmed/1588550>
> -- then there are some other complicated functions based on molecular
fragments and distances among them and to the molecular surface:
> A new approach to analysis and display of local
lipophilicity/hydrophilicity mapped on molecular surfaces.
> Heiden W, Moeckel G, Brickmann J.
> J Comput Aided Mol Des. 1993 Oct;7(5):503-14.
> Estimating and representing hydrophobicity potential
> Fauchere et al.
> Journal of Molecular Graphics
> Volume 6, Issue 4, December 1988, Pages 203-206
> If I understood correctly, these have many parameters and the
functional form is not simple.  It  would not be straightforward to put
them into Chimera.  Finally, I also saw that the program MDL Chime has
something called hydrophobic potential display, but I couldn't find a
description of how it really works  -- it might just be coloring whole
amino acids by hydrophobicity value like Chimera does now, or atoms
based on element.
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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