{"id":12,"date":"2012-04-17T14:31:08","date_gmt":"2012-04-17T14:31:08","guid":{"rendered":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=12"},"modified":"2026-02-06T11:18:48","modified_gmt":"2026-02-06T10:18:48","slug":"pb-align","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pbe\/?page_id=12","title":{"rendered":"PB-ALIGN"},"content":{"rendered":"

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Very fast and efficient structure comparison and mining using protein blocks<\/h2>\n\n\n\n
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PB-ALIGNc<\/h2>\n

PB-ALIGNc is a structure comparison tool.<\/strong> 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.<\/p>\n

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.<\/p>\n

Click here to see a sample PDB file !<\/a><\/p>\n
PBE-ALIGNc<\/span><\/big> (PDB against PDB) <\/span>
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PDB FILE 1<\/span>
\nPDB FILE 2 <\/span><\/p>\n

Local alignment <\/span>
\n Global alignment<\/span>
\n<\/p>\n<\/form>\n<\/td>\n

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PB-ALIGNm<\/h2>\n

PB-ALIGNm is a structure mining tool.<\/strong> 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.<\/p>\n\n

<\/a>PBE-ALIGNm<\/big> (PDB against\u00a0DATABASE )<\/span><\/div>\n

PDB FILE <\/span><\/p>\n

You can also provide your own PB sequence here (in FASTA format<\/a>) : <\/span>
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