Hi Li
I would recommend using Biojava or Biopython for the kind of development
you want to do. Both have a lot of the features that you are looking for
already implemented. For Biojava for instance, I can point you to this
tutorial:
https://github.com/biojava/biojava-tutorial/blob/master/structure/README.md
where you will find some examples and code snippets that can get you
started.
In CCP4 I believe there's a C++ library called MMDB
(http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Mmdb) which
also contains a lot of the features that you are looking for, but I
really don't know many details about it.
Hope this helps
Jose
On 04.03.2015 17:40, Li Xue wrote:
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
<[email protected] <mailto:[email protected]>> 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: [email protected] <mailto:[email protected]>
Web site: http://www.cs.iastate.edu/~lixue/
<http://www.cs.iastate.edu/%7Elixue/>
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: [email protected] <mailto:[email protected]>
Web site: http://www.cs.iastate.edu/~lixue/
<http://www.cs.iastate.edu/%7Elixue/>
