PB-ALIGN

June 27th, 2015

Very fast and efficient structure comparison and mining using protein blocks

PB-ALIGNc

PB-ALIGNc is a structure comparison tool. It compares two protein structures using sequences of PBs combined with classical sequence analysis methods. It first converts protein structures from user’s uploaded PDF files into protein blocks sequences (3D to 1D). It then performs either local (Smith Waterman) or global (Needleman-Wunsch) alignment. Local or global structural similarities can be easily and efficiently identified using PB-ALIGNc. PB-ALIGNc is very fast.

PB-ALIGNc is couple to PROFIT v2.3. After the PB sequences have been aligned, the alignment is used to superimpose the two structures. RMSD is reported and coordinates of superimposed structures can be downloaded.

Click here to see a sample PDB file !

PBE-ALIGNc (PDB against PDB)

PDB FILE 1
PDB FILE 2

Local alignment
Global alignment

PB-ALIGNm

PB-ALIGNm is a structure mining tool. It compares a query structure with all structural domains in SCOP and finds structures that have similar fold to the query. It first converts protein structures from user’s uploaded PDF files into protein blocks sequences (3D to 1D). It then performs either local (Smith Waterman) or global (Needleman-Wunsch) alignment with every structural domains available in SCOP 1.75. Scop domains that share local or global structural similarities with the query are extracted PB-ALIGNc. PB-ALIGNm is fast and takes about 1 min to search for database.

PBE-ALIGNm (PDB against DATABASE )

PDB FILE

You can also provide your own PB sequence here (in FASTA format) :


Choose the database :

Select SCOP class : (select “None” if you are using PDB database)

Select PDB filters : (select “None” if you are using SCOP database)

Length (in %) :

Ranks :

[input number of top alignments in results you would like to see]

Local alignment
Global alignment



To obtain the results of already done query, input the assigned JOBID :

PB-ALIGN group

Swapnil Mahajan, Manoj Tyagi, Priyanka Sharma, Frédéric Cadet, N. Srinivasan, Alexandre G. de Brevern & Bernard Offmann
Site maintained by :S. Mahajan, P. Sharma, M. Tyagi and B. Offmann
Last updated on Saturday, June 27, 2015
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