NPS@ help : Help on work with a sequence - NPSA - Lyon

This site is a fork of the original NPS@ server

November 27th, 2023: NPS@ updated (see NEWS).

Analyse one sequence

When you see the NPSA link in a result page, it allows you to work with a sequence and apply NPS@ methods on it.

You can :

run a sequence similarity search with BLAST or FASTA or PSI-BLAST or SSERACH, the sequence will be the query one
compute a protein secondary structure prediction consensus
analyze protein primary structure (e.g. amino-acid composition, coiled coils prediction, helix-turn-helix detection)

When the sequence comes from a database of protein sequences with known 3-D structures (PDB), more links are available :

to look at PDB entry at PDBe, PDBj, and RCSB.
to download PDB file at NPS@ in ENT format, and at wwPDB in mmCIF and XML formats.
to access PDBSum.
to deduce the secondary structure from 3-D structure by means of DSSP, P-SEA and STRIDE programs.
to search 3-D-based protein classification at : CATH and SCOP database.
to compare 3-D coordinates by means of : DALI.

Last modification time : Wed Feb 15 18:55:07 2023. Current time : Tue Nov 28 11:35:56 2023. User : public@44.220.249.141.