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Amino acid 3D pattern searching in protein structures
The ASSAM program searches for patterns of amino acid side chains in 3D space within PDB structures. The searches are based on distances between the amino side chains which are represented as pseudoatom vectors. This search is independent of the amino acid sequence order.
Citation for referencing ASSAM:
Nurul Nadzirin, Eleanor Gardiner, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W380-6. Epub 2012 May 9. HTML, PDF.
Notes:
1. Your query should be a 3D amino acid pattern which will be used to search for other similar amino acid arrangements in a database of PDB structures.
2. Please ensure that the query is a PDB formatted file.
3. The query file cannot contain more than 12 amino acid residues.
4. An error will be returned for queries exceeding 12 residues including cases where 12 or less residues have multiple positions (ie. from NMR).
5. Queries submitted may take a few minutes to complete, please leave your browser on the page until the results are returned or use the link to retrieve the results (an ASSAM search typically runs for 1-5 minutes depending on the server load).
[see the Help page]
If your input is a protein structure for searching against a pattern or motif database, please use the SPRITE program.
Upload file to submit for ASSAM search:
* PDB input files will not be used for purposes other than the search and will be deleted after 2 days to a week upon search completion.
Precomputed examples:
View precomputed results of ASSAM search of:
4cha_motif.pdb, a 3-residue motif of 4cha, an alpha-chymotrypsin. [View]
2atqRERE_motif.pdb, a 4-residue motif from 2atq, the RB69 single-stranded DNA binding protein-DNA polymerase fusion. [View]
Demonstration run:
Click submit to do a demonstration ASSAM run for 4cha_motif. [Submit]
Please contact info_at_mfrlab.org ( _at_ = @ ) for any queries or to report errors.