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Dear Tim, You can calculate the accesible surface area (ASA) with the program NACCESS. Then you will be able to compare surfaces quantitatively. Cheers, Maria > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Tea and Tim, > > This may be a stupid idea, but what about this: > > 1. Superpose the proteins of interest > 2. Compute their molecular surfaces with msms/Grasp or generate a mask > with an appropriated probe > 3. Take one of these surfaces and "invert it" over a cube defined from a > clipping plane behind your region of interest (so the surface is put > "inwards out" locally; for obvious reasons you cannot do this with all > the surface) > 4. Measure their complementarity with Michael Lawrence's "sc" program > (in ccp4). You might need to translate stepwise if sc doesn't work on > surfaces with clashes. > > Perhaps one of the tools to work with maps/mask could do the inversion? > > Or perhaps it's indeed a stupid idea, after all. > > > Cheers, > > > > > Miguel > > > En/na Tim Gruene ha escrit: >> *** For details on how to be removed from this list visit the *** >> *** CCP4 home page http://www.ccp4.ac.uk *** >> >> >> You can use grasp or msms/Raster3D to calculate and visualise protein >> surfaces. >> But how would you _compare_ surfaces quantitatively? >> >> -- >> Tim Gruene >> Institut fuer anorganische Chemie >> Tammannstr. 4 >> D-37077 Goettingen >> >> GPG Key ID = A46BEE1A >> >> >> On Wed, 21 Jun 2006, Tea Pavkov wrote: >> >>> *** For details on how to be removed from this list visit the *** >>> *** CCP4 home page http://www.ccp4.ac.uk *** >>> >>> >>> Dear ccp4bb, >>> >>> I would like to compare surfaces (not only ligand binding sites) of the >>> proteins within the same family. Do you know if there is a program >>> doing >>> that or do you know people who are involved in developing something >>> like >>> that? >>> >>> Thank you in advance! >>> >>> Tea >>> >>> >>> --------------------------------------------------------- >>> Mag. Pavkov Tea >>> Institute of Chemistry - Structural Biology >>> Karl-Franzens-University Graz >>> Heinrichstrasse 28, 8010 Graz, Austria >>> >>> Phone: ++43 316 380 5414 >>> Fax: ++43 316 380 9850 >>> http://PhysChem.kfunigraz.ac.at/sb >>> --------------------------------------------------------- >>> >> > > - -- > Miguel Ortiz Lombardía > Centro de Investigaciones Oncológicas > C/ Melchor Fernández Almagro, 3 > 28029 Madrid, Spain > Tel. +34 912 246 900 > Fax. +34 912 246 976 > e-mail: [EMAIL PROTECTED] > - ---------------------------------------------------------------------- > Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que > ce qui est fort fût juste. > Blaise Pascal, Pensées > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.1 (Darwin) > > iD8DBQFEmnZBF6oOrDvhbQIRAjIaAJ4qOxFxPbNovZbGyc7XRheQGzkb8wCgp4+2 > 9OUG+U3Wqiz+gK3vNW8aURQ= > =3wVY > -----END PGP SIGNATURE----- >
