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
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
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:
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
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Dear Li,
you find a list of programs with a short description at
http://www.ccp4.ac.uk/dist/html/INDEX.html
1. areaimol: Analyse solvent accessible areas
I am not sure you can reliably derive (partial) side chain charges
from a (X-ray) crystal
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
