title: A structural-based strategy for recognition of transcription factor binding sites.
abstract: Scanning through genomes for potential transcription factor binding sites (TFBSs) is becoming increasingly important in this post-genomic era. The position weight matrix (PWM) is the standard representation of TFBSs utilized when scanning through sequences for potential binding sites. However, many transcription factor (TF) motifs are short and highly degenerate, and methods utilizing PWMs to scan for sites are plagued by false positives. Furthermore, many important TFs do not have well-characterized PWMs, making identification of potential binding sites even more difficult. One approach to the identification of sites for these TFs has been to use the 3D structure of the TF to predict the DNA structure around the TF and then to generate a PWM from the predicted 3D complex structure. However, this approach is dependent on the similarity of the predicted structure to the native structure. We introduce here a novel approach to identify TFBSs utilizing structure information that can be applied to TFs without characterized PWMs, as long as a 3D complex structure (TF/DNA) exists. This approach utilizes an energy function that is uniquely trained on each structure. Our approach leads to increased prediction accuracy and robustness compared with those using a more general energy function. The software is freely available upon request.
authors: Laboratory of Molecular Modeling and Design, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, Liaoning, China.
authors: Beisi
authors: B
authors: Xu
authors: Dustin E
authors: DE
authors: Schones
authors: Yongmei
authors: Y
authors: Wang
authors: Haojun
authors: H
authors: Liang
authors: Guohui
authors: G
authors: Li
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D051188:Knowledge Bases; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D056510:Position-Specific Scoring Matrices; D011487:Protein Conformation; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors