Comparison of proteins based on segments structural similarity

• Autorzy: Plewczynski D. , Pas J. , Von Grotthuss M. , Rychlewski L.
• Języki publikacji: EN

Abstrakty

EN

We present here a simple method for fast and accurate comparison of proteins us­ing their structures. The algorithm is based on structural alignment of segments of Ca chains (with size of 99 or 199 residues). The method is optimized in terms of speed and accuracy. We test it on 97 representative proteins with the similarity mea­sure based on the SCOP classification. We compare our algorithm with the LGscore2 automatic method. Our method has the same accuracy as the LGscore2 algorithm with much faster processing of the whole test set, which is promising. A second test is done using the ToolShop structure prediction evaluation program and shows that our tool is on average slightly less sensitive than the DALI server. Both algorithms give a similar number of correct models, however, the final alignment quality is better in the case of DALI. Our method was implemented under the name 3D-Hit as a web server at http://3dhit.bioinfo.pl/ free for academic use, with a weekly updated database containing a set of 5000 structures from the Protein Data Bank with non-homologous sequences.

Słowa kluczowe

EN

simple method; ToolShop structure; structural hashing; Protein Data Bank; LGscore2 algorithm; C alpha chain; protein structure; LGscore2 automatic method

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2004
• Tom: 51
• Numer: 1
• Opis fizyczny: p.161-172,fig.,ref.

Twórcy

autor

Plewczynski D.

• Warsaw University, Warsaw, Poland

autor

Pas J.

autor

Von Grotthuss M.

autor

Rychlewski L.

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