AL2TS

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 (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

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).

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