ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.
Nucleic Acids Res
; 37(Web Server issue): W396-401, 2009 Jul.
Article
em En
| MEDLINE
| ID: mdl-19483101
ABSTRACT
This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites http//protedna.csbb.ntu.edu.tw/, http//protedna.csie.ntu.edu.tw/, http//bio222.esoe.ntu.edu.tw/ProteDNA/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Software
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Proteínas de Ligação a DNA
Tipo de estudo:
Prognostic_studies
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Risk_factors_studies
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2009
Tipo de documento:
Article