Introduction

iPBA is a tool for comparison of protein structures based on similarity in the local backbone conformation. The local backbone conformation is defined as pentapeptide dihedrals, using Protein Blocks (PBs)[de Brevern et al. 2000, Joseph et al. 2010]. The protein structures represented as PB sequences, are aligned by dynamic programming scored by a PB substitution matrix. Structurally similar stretches are weighed using an anchor based alignment approach.

Compare and align two protein structure

Either upload two PDB files and enter the respective chain IDs or enter both PDB and chain IDs.

Protein 1

   Enter PDB idenfier chain chain
    or
   Upload first structure file: chain



Protein 2

   Enter PDB idenfier chain chain
    or
   Upload second structure file: chain



Advanced option

   Alignment Type:
   Global
   Local

Note that data older than 7 days are deleted.


Search protein similarity in structure database

Either upload the PDB file and the ID of the chain or enter both PDB and chain IDs. This target chain will be compared with domain structures defined under SCOP version 1.75. The default SCOP dataset is filtered at a sequence identity cut-off of 70%. The user can also choose other datasets generated at different cut-offs: 40%, 95% and 100%.



   Enter PDB idenfier chain chain
    or
   Upload first structure file: chain

Choose database

   SCOP sequence identity cutoff:
   40%
   70%
   95%
   100%

Advanced option

   Alignment Type:
   Global
   Local