Literature DB >> 26816396

Knowledge-based three-body potential for transcription factor binding site prediction.

Wenyi Qin1, Guijun Zhao2, Matthew Carson1, Caiyan Jia3, Hui Lu4.   

Abstract

A structure-based statistical potential is developed for transcription factor binding site (TFBS) prediction. Besides the direct contact between amino acids from TFs and DNA bases, the authors also considered the influence of the neighbouring base. This three-body potential showed better discriminate powers than the two-body potential. They validate the performance of the potential in TFBS identification, binding energy prediction and binding mutation prediction.

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Year:  2016        PMID: 26816396      PMCID: PMC8687219          DOI: 10.1049/iet-syb.2014.0066

Source DB:  PubMed          Journal:  IET Syst Biol        ISSN: 1751-8849            Impact factor:   1.615


  30 in total

1.  Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.

Authors:  N M Luscombe; R A Laskowski; J M Thornton
Journal:  Nucleic Acids Res       Date:  2001-07-01       Impact factor: 16.971

2.  A structure-based method for derivation of all-atom potentials for protein folding.

Authors:  Edo Kussell; Jun Shimada; Eugene I Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-09       Impact factor: 11.205

3.  Geometric cooperativity and anticooperativity of three-body interactions in native proteins.

Authors:  Xiang Li; Jie Liang
Journal:  Proteins       Date:  2005-07-01

4.  A knowledge-based orientation potential for transcription factor-DNA docking.

Authors:  Takako Takeda; Rosario I Corona; Jun-Tao Guo
Journal:  Bioinformatics       Date:  2012-12-05       Impact factor: 6.937

5.  Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes.

Authors:  Mario Pujato; Fabien Kieken; Amanda A Skiles; Nikos Tapinos; Andras Fiser
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 16.971

6.  Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction.

Authors:  Rafik A Salama; Dov J Stekel
Journal:  Nucleic Acids Res       Date:  2010-05-03       Impact factor: 16.971

7.  An all-atom knowledge-based energy function for protein-DNA threading, docking decoy discrimination, and prediction of transcription-factor binding profiles.

Authors:  Beisi Xu; Yuedong Yang; Haojun Liang; Yaoqi Zhou
Journal:  Proteins       Date:  2009-08-15

8.  Protein-DNA binding specificity predictions with structural models.

Authors:  Alexandre V Morozov; James J Havranek; David Baker; Eric D Siggia
Journal:  Nucleic Acids Res       Date:  2005-10-24       Impact factor: 16.971

9.  RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

Authors:  Heladia Salgado; Martin Peralta-Gil; Socorro Gama-Castro; Alberto Santos-Zavaleta; Luis Muñiz-Rascado; Jair S García-Sotelo; Verena Weiss; Hilda Solano-Lira; Irma Martínez-Flores; Alejandra Medina-Rivera; Gerardo Salgado-Osorio; Shirley Alquicira-Hernández; Kevin Alquicira-Hernández; Alejandra López-Fuentes; Liliana Porrón-Sotelo; Araceli M Huerta; César Bonavides-Martínez; Yalbi I Balderas-Martínez; Lucia Pannier; Maricela Olvera; Aurora Labastida; Verónica Jiménez-Jacinto; Leticia Vega-Alvarado; Victor Del Moral-Chávez; Alfredo Hernández-Alvarez; Enrique Morett; Julio Collado-Vides
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

10.  Prediction of TF target sites based on atomistic models of protein-DNA complexes.

Authors:  Vladimir Espinosa Angarica; Abel González Pérez; Ana T Vasconcelos; Julio Collado-Vides; Bruno Contreras-Moreira
Journal:  BMC Bioinformatics       Date:  2008-10-16       Impact factor: 3.169

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  1 in total

1.  Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model.

Authors:  Ke Tang; Jorjethe Roca; Rong Chen; Anjum Ansari; Jie Liang
Journal:  J Biol Phys       Date:  2022-04-20       Impact factor: 1.560

  1 in total

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