Dear Dr. Vriend, Thanks for your reply and the resources that you suggested.
My background is computer science and I am working on protein interface predictions. The questions that I asked are standard processing steps in protein interface predictions. But nobody in my field have used a *platform* to calculate and integrate them into different classifiers. Different classifiers use different features and have different processing details. I just thought it would be convenient, for both development and maintenance, to build classifiers on one platform that have all the functionalities. A senior PhD student in X-ray told me that ccp4 is a very powerful platform and should have all the functionalities that I need (but he himself does not really know). So following his suggestion, I am checking it out on ccp4bb to see whether it is a platform that I am looking for. Thanks again for your reply. I will also check http://swift.cmbi.ru.nl/gv/facilities/. It is nice to know that some calculations are already routinely done on the whole PDB. It will be a very good resource for us to develop algorithms. Regards, Li On Wed, Mar 4, 2015 at 2:06 PM, Gert Vriend <gerrit.vri...@radboudumc.nl> wrote: > Dear Li Xue, > > The questions you are asking are more the domain of protein structure > bioinformatics than X-ray crystallography. The CCP4 has a series of these > programs available, but their collection is limited. May I suggest that you > also look at http://swift.cmbi.ru.nl/gv/facilities/. There you can find > pointers to a series of web servers that do things like you ask with PDB > files as input. Most of the web servers are also available as a web service > that you can call directly from your software. Further, several of the > calculations you ask for we routinely perform once per week on all new PDB > files and store the results in easy-to-parse files, one per PDB file. > > Greetings > Gert > On 03/04/2015 11:20 AM, Li Xue wrote: > > Hi, > > I am new to ccp4. I am writing to check the possibility to use ccp4 as a > platform to develop my software. > > I was wondering whether I could get the following information from ccp4 after > I input a pdb file: > > 1. chemico-physical properties of each residue, such as hydrophobicity, > side chain charge, relative solvent accessibility and so on. > 2. the nearest 5 neighbor residues of each residue in the pdb file > > 3. add hydrogen to the pdb file > > Although I can calculate the above information myself without using ccp4, > it would be great thatccp4 has already all the packages that I need. I'd > appreciate it very much if someone could point out where I should start > with. > > Thanks. > > Li > > > -- > Xue, Li > Bijvoet Center for Biomolecular Research > Utrecht University > Email: l....@uu.nl > Web site: http://www.cs.iastate.edu/~lixue/ > > > Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het > handelsregister onder nummer 41055629. > The Radboud university medical center is listed in the Commercial Register > of the Chamber of Commerce under file number 41055629. > -- Xue, Li Bijvoet Center for Biomolecular Research Utrecht University Email: l....@uu.nl Web site: http://www.cs.iastate.edu/~lixue/
