Danilo, There are two points that I want you to consider before I attempt to answer your question:1. In terms of capabilities:Voidoo has the capability to detect specific voids or all voids inside a bio-macromolecular complex, as well as certain cavities that are connected to the "outside world". It delineates these cavities, meaning that it finds their extent in 3-dimensional space. Secondly, it measures the molecular volumes as well as the volume of the cavity itself. Finally, it has the capability to generate molecular surface plot files which enable the visualization of the cavities. Voidoo will detect voids and invaginations, but it cannot pick pockets, no pun intended :)2. In terms of measuring and displaying cavities, there are three particular modes:a. Vanderwaals cavity, where the cavity comprises the compliment of the Vanderwaals surface of the surrounding atoms.b. Probe-accessible cavity, where the cavity comprises all of the space that can be accessed by the center of the probe sphere.c. Probe-occupied cavity, where the cavity comprises all of the space that can be occupied by the probeNow to answer your question:The first step of the cavity detection algorithm is to map the target molecule onto a 3-dimensional grid with a spacing (0.5 - 1 Angstrom). All of the grid points are initially assigned a value of zero. Every subsequent point of the grid whose distance to the nearest atom is less than the sum of the van der Waals radius of that atom and the probe radius, is assigned a value of 1. In order to exclude the outside world, all of the grid points on the faces of the grid are set to zero, and the outside world is "zapped".This method is also known as the "flood fill" algorithm. At the final stage, all grid points are inside a closed cavity and have a value of zero. Voidoo then checks if the cavity has been detected and will delineate the cavity to measure the volume. Then the process of "atomic flattening" is invoked, which entails multiplying the van der Waals radii of all atoms by a certain flattening factor. The program then goes through iterative rounds of atomic flattening to close off cavities which are in contact with the outside world, and separate cavities which are in contact with each other through small channels. The program will stop after the particular sought after cavity has been found. A detailed answer to your question can be found in the original resource that I sent in my first response:http://journals.iucr.org/d/issues/1994/02/00/gr0263/gr0263.pdfI hope this helps!lorenzoLorenzo Ihsan FInci, Ph.D.Postdoctoral Scientist, Wang LaboratoryHarvard Medical SchoolDana-Farber Cancer InstituteBoston, MA Peking UniversityThe College of Life SciencesBeijing, China
> Date: Fri, 10 Aug 2012 10:39:29 +0200 > From: danilo.belv...@ic.cnr.it > To: lfi...@hotmail.com > Subject: RE: [ccp4bb] calculation of cavities within crystal protein > > Thanks you for your help Lorenzo. > VOIDOO seems to be the proper software for this calculation, and it is > suggested by many people. > > I am not an expert in this field! So, I would have only one thing to > ask, because of a doubt arising from what I read in > http://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf. > > In the paper, VOIDOO is a "grid-based procedure that measures the > cavity volume defined by the van der Waals surface of atoms lining the > cavity" > Does this mean that van der Waals surfaces of a protein and the > surrounding proteins are considered in the calculation? > > I hope not too disturbing you. > > Danilo > > On Thu, 9 Aug 2012 10:05:19 -0400, "Dr. Lorenzo Finci" > <lfi...@hotmail.com> wrote: > > 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_VOIDOO > > http://binf.gmu.edu/ttaylor/DELAUNAY_PAPERS/chakravarty1.pdf > > > > I hope this helps! > > lorenzo > > > > Lorenzo Ihsan FInci, Ph.D. > > Postdoctoral Scientist, Wang Laboratory > > Harvard Medical School > > Dana-Farber Cancer Institute > > Boston, MA > > Peking University > > The College of Life Sciences > > Beijing, 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 >
