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Tosatto, Silvio CE and Battistutta, Roberto (2007) TAP score: torsion angle propensity normalization applied to local protein structure evaluation. [Online journal papers]

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Per gentile concessione di: http://www.biomedcentral.com/1471-2105/8/155

Abstract (english)

Background

Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging.

Results

A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at http://protein.cribi.unipd.it/tap/ webcite.

Conclusion

A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination.


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EPrint type:Online journal papers
Anno di Pubblicazione:2007
Key Words:protein model, protein structure evaluation
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Dipartimenti > Dipartimento di Scienze Chimiche
Codice ID:1212
Depositato il:09 Dec 2008
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