Danilo,
The protein cavity can be analyzed utilizing the program Voidoo ( Kleywegt GJ,
1994). This program uses an atomic-flattening algorithm based on a
3-dimensional grid to locate and delineate different cavities. A Van Der Waals
cavity can further be generated with a probe radius with a computed cavity grid
using the highest number of grid points, and a contact and accessible surface
can further be evaluated...
Relevant
Resources:http://pelican.rsvs.ulaval.ca/mediawiki/index.php/Analysing_protein_cavities_using_VOIDOOhttp://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf
I hope this helps!lorenzo
Lorenzo Ihsan FInci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard
Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityThe
College of Life SciencesBeijing, China
> Date: Thu, 9 Aug 2012 13:53:09 +0200
> From: danilo.belv...@ic.cnr.it
> Subject: [ccp4bb] calculation of cavities within crystal protein
> To: CCP4BB@JISCMAIL.AC.UK
>
> Dear all,
>
> I am Dr. Danilo Belviso and I am working on a platinum-based inhibitor
> for matrix-metallo proteasis.
>
> I have obtained the crystal structure of the adduct Pt/protein and, for
> me, would be very interesting to know the cavities of the protein within
> the crystal, namely by considering symmetry-related protein molecules
> around the asymmetric unit.
>
> Do you know a software (or server) that carries out this calculation?
>
> Best regards
>
> Dr. Danilo Belviso
