VMD-L Mailing List

From: Francesco Oteri (francesco.oteri_at_gmail.com)
Date: Sun May 29 2011 - 07:09:59 CDT

Hi all,
program like VOIDOO (http://xray.bmc.uu.se/usf/voidoo.html) SURFNET
(http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
<http://www.biochem.ucl.ac.uk/%7Eroman/surfnet/surfnet.html>) and CAVER
(http://www.caver.cz/)
are able to locate protein cavities. Maybe they are sutable for you
purpose.
In particular, I usually use SURFNET. It produces a pdb file where each
atom is a sphere matching cavities.

Francesco

Il 29/05/2011 10:17, Axel Kohlmeyer ha scritto:
> On Sun, May 29, 2011 at 12:26 AM, BRAULIO VALDEBENITO MATURANA
> <bvaldebenito09_at_alumnos.utalca.cl> wrote:
>> Thanks for the answers, but what we really want to know is (or if you could
>> pinpoint us to a site where this is explained) how exactly are those density
>> values in the .dx file related to the atoms in the pdf file, I mean, if
>> there are some zeros on the first file, how could I be able to tell which
>> x,y,z coordinates do they match?
> the correlation of the gridpoint values and the coordinates can be
> optained from the header of the respective files. for DX files, see:
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html
>
> this is just a regular 3d grid.
>
>> We have already looked into tools like CASTp, CSPro, McVol, etc., and they
>> all use some geometrial approach to solve this problem, like "Delaunay
>> Triangulation" or using probe spheres. We would like to develop a script
>> that let us to get a "crude" estimate, like you said. We're in college, and
>> this is the main task for one of our courses, you could think of this as
>> something "binary", in the way that the output of the script should say if
>> there are cavities, where they are, and a rough estimate of their volume.
> things are not as easy as you might think. you have to be able to
> tell whether you are inside of a protein or on the surface and that
> can be _really_ difficult. think of having a molecule with a "deep"
> pocket. when would it belong to the surface, and when inside?
>
> cheers,
> axel.
>
>
>> Cheers,
>> Braulio.
>>
>>> --------------------------------------------------
>>> From: "John Stone"<johns_at_ks.uiuc.edu>
>>> Sent: Friday, May 27, 2011 3:47 PM
>>> To: "BRAULIOFAVIÁNVALDEBENITO MATURANA"<bvaldebenito09_at_alumnos.utalca.cl>
>>> Cc:<vmd-l_at_ks.uiuc.edu>
>>> Subject: Re: vmd-l: Protein cavities
>>>
>>>> Hi,
>>>> The DX files are a visualization file format that can also be used to
>>>> store
>>>> uniform grids of scalar data, which is what the 'volmap' commands do.
>>>> If you compute a density map from your structure, you'll get density
>>>> values
>>>> of zero at the points associated with empty space, so that is a very
>>>> simple
>>>> way to determine where you have pockets or cavities of empty space.
>>>> You could get a crude estimate of empty volume from this kind of
>>>> approach,
>>>> but I should also point out that with a little google searching, that
>>>> I think that there are tools available that are specifically designed to
>>>> find cavity volumes. So, before you implement it yourself in a VMD
>>>> script, I would suggest googling for 15 or 20 minutes and see if you can
>>>> find one of those tools. I seem to remember I've heard of a couple such
>>>> programs in the past, but I don't remember them anymore.
>>>>
>>>> Cheers,
>>>> John Stone
>>>> vmd_at_ks.uiuc.edu
>>>>
>>>>
>>>>
>>>> On Thu, May 26, 2011 at 05:41:48PM +0000, BRAULIO FAVIÁN VALDEBENITO
>>>> MATURANA wrote:
>>>>> Dear all,
>>>>>
>>>>> We're working on a Tcl/Tk script whose function is to determine both
>>>>> surface and internal cavities of a given protein. In order to achieve
>>>>> that, we've been thinking in the "volmap" function as stated by John
>>>>> Stone
>>>>> in reply to "cavity/pocket representation" on May 2nd, 2006 (it can be
>>>>> seen here:
>>>>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/6885.html), but
>>>>> instead of a graphical output, we need the analytical data too.
>>>>>
>>>>> Well, regarding the output of the "volmap" command, which is a file
>>>>> with
>>>>> .dx extension, we would like to know if there is any way to use the
>>>>> information on that file so that we can "substract" from the entire
>>>>> map
>>>>> the volume occupied by the actual molecule, thus letting the volume of
>>>>> any
>>>>> possible cavities.
>>>>>
>>>>> Thanks in advance!
>>>>> Braulio.
>>>> --
>>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>>> Beckman Institute for Advanced Science and Technology
>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>>> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>>>>
>
>