Hi there … I’m currently investigating how to use Jalview and DAS to annotate functional residues in protein domains. I give Jalview my own multiple protein sequence alignments.
A given protein sequence in the alignmment may, or may not, include the whole of a protein chain… Because I won’t always be using a whole protein chain, is there a way of mapping the residue numbering as contained in the pdbs of these protein domains with the multiple sequence alignment in Jalview?
Might I be able to achieve this by mapping each sequence to its associated protein domain (which I can provide as a pdb file) or is there another way to do this (if its possible at all).
Hi there .. I'm currently investigating how to use Jalview and DAS to annotate functional residues in protein domains. I give Jalview my own multiple protein sequence alignments.
A given protein sequence in the alignmment may, or may not, include the whole of a protein chain.. Because I won't always be using a whole protein chain, is there a way of mapping the residue numbering as contained in the pdbs of these protein domains with the multiple sequence alignment in Jalview?
If you right click on a sequence and follow the Structure->Associate Structure submenu you can select 'From file' to load your own PDB file onto the sequence. Jalview will map the residues in the structure to the displayed sequence via a global pairwise alignment.
Unfortunately, there is no way, currently, to do this in bulk - i.e. say 'associate all the pdb files in this directory to their closest homologs in the alignment'. This is a feature which we hope to implement some time in the future.
Might I be able to achieve this by mapping each sequence to its associated protein domain (which I can provide as a pdb file) or is there another way to do this (if its possible at all).
If your proteins are in Uniprot, the easiest way is to name your sequences with their Uniprot IDs. The 'Fetch DB Refs' function under the web service menu will then correct the start/end numbering against the uniprot record, and add any PDB cross references automatically. This at least means that you can view DAS features via the uniprot coordinate system. The latest development version of jalview also supports PDB ids as a coordinate system (enabling the two or three DAS services which support PDB id queries such as the dssp service).
Is that what you mean ?
Jim.
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J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Perhaps I should explain what I’m trying to do a bit more.
I’m basically wanting to annotate protein structure alignments with those residues that are involved in ligand binding and also those residues that are catalytic residues… I have my own DAS server that links to a database containing my residues of interest. This works brilliantly when I use protein alignments of whole chains. But I also need it to work at the protein domain level - hence why I need a way of ensuring that the residue numbers as observed by the PDB are recognised by Jalview.
Hi there … I’m currently investigating how to use Jalview and DAS to annotate functional residues in protein domains. I give Jalview my own multiple protein sequence alignments.
A given protein sequence in the alignmment may, or may not, include the whole of a protein chain… Because I won’t always be using a whole protein chain, is there a way of mapping the residue numbering as contained in the pdbs of these protein domains with the multiple sequence alignment in Jalview?
If you right click on a sequence and follow the Structure->Associate Structure submenu you can select ‘From file’ to load your own PDB file onto the sequence. Jalview will map the residues in the structure to the displayed sequence via a global pairwise alignment.
Unfortunately, there is no way, currently, to do this in bulk - i.e. say ‘associate all the pdb files in this directory to their closest homologs in the alignment’. This is a feature which we hope to implement some time in the future.
Might I be able to achieve this by mapping each sequence to its associated protein domain (which I can provide as a pdb file) or is there another way to do this (if its possible at all).
If your proteins are in Uniprot, the easiest way is to name your sequences with their Uniprot IDs. The ‘Fetch DB Refs’ function under the web service menu will then correct the start/end numbering against the uniprot record, and add any PDB cross references automatically. This at least means that you can view DAS features via the uniprot coordinate system. The latest development version of jalview also supports PDB ids as a coordinate system (enabling the two or three DAS services which support PDB id queries such as the dssp service).
Is that what you mean ?
Jim.
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.