Is There Any Software/Server Which Can Give Missing Residues Of Pdb Files?
3
1
Entering edit mode
9.7 years ago
Sagar Nikam ▴ 160

i finds thousands of files in protein data bank,in which many chains have missing residues it creates problem while calculating phi & psi

also another problems:- there are some residues in chain ,where one of atom type e.g.N, CA, C, O (which are essential for phi/psi calculations) are not given/absent

what should i do? any logic/program/server......

pdb • 6.0k views
ADD COMMENT
2
Entering edit mode
9.7 years ago

The way I have dealt with this problem is to use Modeller (http://salilab.org/modeller/) to "impute" missing residues and atoms. It is not a trivial task (you have to write code), but this should get you started:

http://salilab.org/archives/modeller_usage/2002/msg00188.html

ADD COMMENT
0
Entering edit mode

The post from that modeller_usage mail list uses outdated modeller interface. Besides adding missing residues to PDB structures by modeling (de novo) make sense only in some applications. If 'true' phi/psi angles from PDB are needed, for example for statistical analysis, modeling by Modeller does not make sense.

ADD REPLY
2
Entering edit mode
9.7 years ago
Jan Kosinski ★ 1.6k

If PDB structure has a missing residue you just don't calculate phi/psi angles for neighboring residues...

In a case you want to derive some statistics about phi & psi angles in protein structures, one direct solution to your problem is to use high resolution structures only. Such structures should have much less missing atoms. For that kind of analysis you should use high resolution structures only anyway as low resolution ones will have more uncertainties/errors.

For cases where a residue is not missing but some of its atoms are missing, perhaps you can add missing atoms using Modeller's complete_pdb() (http://salilab.org/modeller/manual/node432.html). This will not work however for adding whole missing residues.

BTW. the missing residue information is included in pdbx_poly_seq_scheme field in mmCIF as questions marks . Also, this information is directly accessible through SEQATOMS database

ADD COMMENT
0
Entering edit mode
6.3 years ago

Anyone who is having the same problem, Please use http://lorentz.dynstr.pasteur.fr

ADD COMMENT

Login before adding your answer.

Traffic: 2009 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6