Introduction

mulPBA 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 [Joseph et al. 2011]. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment. Highly similar stretches identified by the pairwise alignments are given higher weights during the progressive alignment. Encoding the information on backbone conformation as PB sequences, enables 'sequence-like' structural alignment, which is minimally influenced by structural flexibility (see examples). The residue equivalences from PB based alignments are identified to obtain a three dimensional fit of the structures, followed by an iterative refinement of the structural superposition.

Compare and align multiple protein structure - PDB data

Use this form to analyse chain from Protein Data Bank files. In order to make multiple protein analysis a minimum of 3 protein are required. The files can also be uploaded see bellow.

Protein Data Bank uploader





Data have to be formatted as below: PDBCODECHAIN.
Separate identifiers by a newline or a space


Compare and align multiple protein structure - files analysis

Upload PDB files and enter the respective chain IDs.
The files can be uploaded as an archive see bellow.

Personal PDB files:


 chain 


Note that data upload is limited to 50 Mb.
The first 4 letters of the files name have to correspond with the PDB code.


Compare and align multiple protein structure - archive file

You can upload archive containing all your pdb files (zip, tar, tar.gz, tgz and gz).

Proteins archive


 chain 


Note that data upload is limited to 50 Mb and the number of files have to be between 3 and 20.
Chain identifier is considered as the same for all the files.
The first 4 letters of the files name have to correspond with the PDB code.


Compare and align multiple protein structure - archive

You can use your analysis number to reprint analysis.

Analysis archive


Analysis ID:


Note that analysis older than 7 days are deleted. To found your analysis ID :
http://www.dsimb.inserm.fr/dsimb_tools/mulpba/TMP/mulpba.20120507081426_88772/results.html