PDB file from primary protein sequence

Bill_A_Nussbaumer at bd.com Bill_A_Nussbaumer at bd.com
Wed Apr 17 20:13:01 EST 2002

If you're only predicting the secondary structure then there's no need take
things as far as a PDB file viewed in RasMol.  However if your protein is
(though I assume it isn't), look for the structure in the protein data bank (http://www.rcsb.org/pdb/).

To attempt a prediction of the protein's secondary structure try the PredictProtein server:  http://dodo.cpmc.columbia.edu/pp/
For more information on secondary structure try this site:  http://www.cryst.bbk.ac.uk/PPS2/course/section8/index.html

For a prediction of the tertiary structure you can try to submit to http://www.expasy.ch/swissmod/SWISS-MODEL.html
Be careful interpreting the results however, such ab initio methods in structure prediction may not be reliable.

For tertiary structure prediction you may also want to subject your sequence, predicted motifs, domains and tertiary structure to alignments with
known proteins.
Pick through the list of software here:


Good Luck.  Sorry I can't be more help but hopefully this will get you started.

- Bill Nussbaumer

mohitbhatiache at hotmail.com wrote:

Sent by:  owner-comp-bio at hgmp.mrc.ac.uk

To:   bionet-biology-computational at moderators.isc.org
Subject:  PDB file from primary protein sequence

I am a final year student of chemical and bio engineering.
I am working on predicting secondary structure of protein from its
primary base pair sequence ie Primary structure. I want to know:
how can i obtain PDB file form my primary protein sequence so that i
can run that in RASMOL
Mohit Bhatia

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