Protein Block Expert (PBE) -- a web-based protein structure analysis server using a structural alphabet

URL:

What you can do:

Conduct protein structure analysis and comparison using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet.

Highlights:

This web server is aimed to provide a platform for protein structure analysis using well defined library of short structural motifs(SSMs) known as structural alphabets (SA).
It uses a set of 16 SSMs called Protein Blocks (PBs) and a PB substitution matrix derived from large set of structurally aligned homologous proteins present in PALI Database.
The Web server provides several software tools to perform the following:
** PB sequence alignment between two proteins to identify local structural similarities [PBE-ALIGN]
** Extraction of similar fold proteins from databank for a given query protein [PBE-ALIGN]
** PB sequence databank containing protein domains from SCOP encoded into PBs [PBE-SAdb(sequence)]
** Pair-wise PB sequence alignment databank for each SCOP class [PBE-SAdb(alignment)]
** Transformation of 3D conformation of a protein structure into 1D sequence of PBs [PBE-T]

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Literature & Tutorials:

This record last updated: 04-21-2014