[BiO BB] Structure/Sequence Alignment

[Michel Dumontier]

Pankaj,
  Try using ClustalW.  It lets you load in the structure template's
secondary structure as a numeric profile that weighs position-specific gap
penalties.  This typically forces gaps into unstructured regions of the
protein structure.  You can make a multiple sequence alignment of the
sequences and then generate a profile-profile alignment.

-=Michel=-


----- Original Message ----- 
From: "Pankaj" <pankaj at nii.res.in>
To: <bio_bulletin_board at bioinformatics.org>
Sent: Tuesday, January 06, 2004 10:35 AM
Subject: [BiO BB] hi


> hi all,
> i m a new member of this board.
> i have a 3 protein structures (all taking the same fold) with the
> substrate bound. the residues surrounding the substrate are the active
> site residues. now i have a set of 400 protein sequences which i know
> take the same above mentioned fold. i want to extract the active site
> residues from these 400 sequences. but whatever alignment program i
> use either uses only sequence information or only structure
> information. is there an alignment program which can use both
> structure and sequence information for the alignment of these 400
> sequences on the strcutural template
>