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synopsis

Superimposé is a framework for superposition that enables a flexible execution of tasks on valuable data sources -
from protein structure alignment to in silico screening.

Tasks related to Superimposé server:

• Discovering known drug active compounds similar to a given molecule.
• Checking if a given ligand is already bound to an entry in the pdb.
• Discovering new binding sites in the pdb with a template.
• Screening for similarity of proteins.

Datasources available for structural comparison and screening:

• PDB as cuĺled Version from the pisces server
• a "hull only" version of the PDB as culled version from the pisces server
• Official NCI data with 25 conformers on average per molecule
• Ligand Depot (ligands bound to PDB proteins)
• Superdrug drug database with 40 conformers on average

In the documentation you can find more information about databases, algorithms, applications. and the options for visualization we provide.

First time users

Especially for first time users we recommend to lean back and watch the guided tour through Superimposé. After that you should check out our examples to get a feeling for the way Superimposé works in reality. With that knowledge in mind it should be easy to use your own data with Superimposé. Feedback is welcome!

news

2008-05-09 database update on the way - please be patient
2008-05-09 ligand depot now renamed ligand expo (under the pdb umbrella) => preparing switch
2008-04-29 Superimpose is being on show at the Galician Bioinformatics Network (thanks Arno!)
2008-04-09 new version 1.1.7. a lot of issues fixed and improved (see changelog.txt)
2008-04-01 database update successfully performed
2008-02-29 database update successfully performed
2008-02-19 update to 1.1.5: faster haystack, updated examples, some minor fixes
2008-02-15 update to 1.1.4: better haystack parameterset, astral gangsta feature fixed
2008-02-12 update to 1.1.3: ASTRAL, improved Score1 parameterset, haystack bug solved, Gangsta sorting solved
2008-01-28 update to 1.1.1: improved small-small parameterset. fixed gangsta visualization bug.
2008-01-23 DONE: NEW VERSION 1.1. FINAL TESTS ARE CURRENTLY BEING PERFORMED (SCHEDULED 2008-01-22 AND 23). Please be patient.