AL2TS

From
sequence-structure ALignment to Tertiary Structure

AL2TS service is designed to generate tertiary structure (3D model) for a given sequence-structure alignment model. If you don't have sequence-structure alignment data for your sequence of amino-acids then you can use AS2TS server to search for the homologues proteins in PDB and then build a 3D model.

AL2TS service provides the possibility to translate sequence-structure alignment data (HELP; see example): 

MODEL   Name of the model (Query)
1WDN_A  PDB code of the chain of protein used as a template (Subject)

Query:  ----RKNGLNVKMDYTPNSGQLVRNLLNGKYNIAVAGIDNVIAYQEGQVKEPVVNPDMFAFYGV
Sbjct:  AAIAKELKLDYELKP-MDFSGIIPALQTKNVDLALAGITIT--------DERKKAIDFSDGYYK

Query:  DNGLLSLVA-NPQIKNISDLKGKQVSVDALTTG
Sbjct:  SGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGS
to tertiary structure (coordinates) version of the protein model:   MODEL

Please check HELP for more information about format requirements.

  (Optional) name of the model (Query).
  PDB code of the chain of protein used as a template (Subject).
In the example above the single PDB entry 1wdn chain A was used (use notation _A to indicate chain A ).

Paste or type your alignment data into the box below (AL format or 'Query:' and 'Sbjct:' records).

Start atom numbering   and residue numbering   in the translated 3D structure (in the model).
BLAST format of the alignment:    NO   YES        AL format - residue renumbering

Side-chains building procedure (SCWRL ):    NO    SCWRL    IDres+SCWRL

Note: Sometimes side-chains calculations can take several minutes. When IDres+SCWRL option is selected, then identical residues are copied from the template to the model, and the Scwrl program is used to calculate side chain atom positions for remaining residues only.

Please send any comments or suggestions concerning
the AL2TS facility to Adam Zemla : adamz@llnl.gov