DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Abstract Text:

Harianto Tjong,Huan-Xiang Zhou,

Structural and physical properties of DNA provide important constraints on the binding sites formed on surfaces of DNA-targeting proteins. Characteristics of such binding sites may form the basis for predicting DNA-binding sites from the structures of proteins alone. Such an approach has been successfully developed for predicting protein-protein interface. Here this approach is adapted for predicting DNA-binding sites. We used a representative set of 264 protein-DNA complexes from the Protein Data Bank to analyze characteristics and to train and test a neural network predictor of DNA-binding sites. The input to the predictor consisted of PSI-blast sequence profiles and solvent accessibilities of each surface residue and 14 of its closest neighboring residues. Predicted DNA-contacting residues cover 60% of actual DNA-contacting residues and have an accuracy of 76%. This method significantly outperforms previous attempts of DNA-binding site predictions. Its application to the prion protein yielded a DNA-binding site that is consistent with recent NMR chemical shift perturbation data, suggesting that it can complement experimental techniques in characterizing protein-DNA interfaces.

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Publishing Authors By Initials

H Tjong,HX Zhou,

For similar investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research abstracts see: investigative techniques: genetic techniques: sequence analysis: sequence analysis, protein research

PUBMED ID PMID:

MEDLINE DATE:

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Nucleic acids research

VOLUME: 35

Page Numbers: 1465-77

Journal Abbreviation:

ISSN: 1362-4962

DAY: 6

MONTH: 02

YEAR: 2007

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 411011

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Keywords Mesh Terms:

KEYWORDS: Sequence Analysis, Protein

MESH TERMS: chemistry

Chemical & Substance for Abstract: DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. Information

Substance Name: DNA

Registry Number: 9007-49-2

Grant and Affiliation Information for DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

AFFILIATION: Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA.

Country: England

AGENCY: United States NIGMS

GRANT: GM58187

ACRONYM: GM

MEDLINETA: Nucleic Acids Res

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces Related Publications

• Inhibitors of Na+/H+ and Na+/Ca2+ exchange depress intracellular calcium elevation induced by ischemia/reperfusion in rat cardiac myocytes.
• Inhibitory effect of recombinant FN polypeptide CH50 on the metastasis and tumor growth.
• Quantification of bcr/abl mRNA expression level in leukemia cells by FQ-RT-PCR.
• [An experimental study on the survival of the anterior abdominal skin flap after VEGF cDNA administration]
• [An inquiry into blood loss in laparoscopic liver resections]
• [Association studies of dopamine D4 receptor gene and dopamine transporter gene polymorphisms in Han Chinese patients with attention deficit hyperactivity disorder]
• [Beneficial effect of thyrotropin-releasing hormone in combination with HSD on hemorrhagic shock with pulmonary edema at high altitude in the rat]
• [Changes in platelet membrane glycoprotein levels in patients with cardiopulmonary resuscitation]
• [Clinical analysis of 13 infected total knee replacements]
• [Detection of epileptic waves in EEG based on wavelet transform]
• [Effects of Alexandrium tamarense and Prorocentrum donghaiense on rotifer Brachionus plicatilis population]
• [Effects of the novel gene, LAPTM4B, highly expression in hepatocellular carcinoma on cell proliferation and tumorigenesis of NIH3T3 cells]
• [Experimental study of K562 cell apoptosis induced by harringtonine]
• [Expression of otsA gene in tobacco and improvement stress tolerance]
• [Hemodynamic and pathologic changes in open abdominal wound after seawater immersion in dog]
• [High efficient expression of recombinant human platelet factor IV in pichia pastoris]
• [Identification of radix Rubiae and the root of Humulus scardens (Lour.) Merr.]
• [Incompatibility among indigenous plasmids of Sinorhizobium fredii strains and its application for plasmid curing]
• [Nutrition support of severe illness patients of general surgery during perioperation period]
• [Preliminary analysis of the characteristics of red tide areas in Changjiang River estuary and its adjacent sea]
• [Relationship between tissue inhibitors of metalloproteinase and metastasis and prognosis in breast cancer]
• [Repairing large alar defects by using a retro-grade auricular flap]
• [Research advance in effects of harmful algal bloom species on zooplankton]
• [Scoring protocol for quantitative diagnosis of gastrointestinal dysfunction and failure in severe cases]
• [Study on new techniques for genetic diagnosis of deletional alpha-thalassemia]
• [The influence of intrahepatic transplantation of hepatocytes and insular cells on liver cirrhosis]
• [The relationship of facet orientation to intervertebral disc protrusion and lateral recess stenosis in lower lumbar spine]
• [Transplantation of bone marrow cells upregulated vascular endothelial growth factor and its receptor and improved ischemic myocardial function]
• [Ultrasound surveillance of cervical lymph node metastasis in thoracic esophageal carcinoma]
• [Using scar tissue flap to repair secondary nasal deformities of unilateral cleft lip]