Literature DB >> 16427316

Prediction of MEF2A-DNA interface by rigid body docking: a tool for fast estimation of protein mutational effects on DNA binding.

Francesca Fanelli1, Stefano Ferrari.   

Abstract

The protein-protein docking algorithm ZDOCK has been challenged for the first time to predict protein-DNA contacts. The computational approach defined in this study has proven effectiveness in fast in silico estimations of mutational effects of the MEF2A transcription factor on DNA binding.

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Year:  2006        PMID： 16427316     DOI： 10.1016/j.jsb.2005.12.002

Source DB:  PubMed          Journal:  J Struct Biol        ISSN： 1047-8477            Impact factor:   2.867


  18 in total

1.  Stability and binding properties of a modified thrombin binding aptamer.

Authors:  Bruno Pagano; Luigi Martino; Antonio Randazzo; Concetta Giancola
Journal:  Biophys J       Date:  2007-09-21       Impact factor: 4.033

Review 2.  What in silico molecular docking can do for the 'bench-working biologists'.

Authors:  Marius Mihăşan
Journal:  J Biosci       Date:  2012-12       Impact factor: 1.826

3.  Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.

Authors:  Howook Hwang; Thom Vreven; Brian G Pierce; Jui-Hung Hung; Zhiping Weng
Journal:  Proteins       Date:  2010-11-15

4.  Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.

Authors:  Xianjin Xu; Liming Qiu; Chengfei Yan; Zhiwei Ma; Sam Z Grinter; Xiaoqin Zou
Journal:  Proteins       Date:  2016-12-02

5.  Structural models of protein-DNA complexes based on interface prediction and docking.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  Curr Protein Pept Sci       Date:  2011-09       Impact factor: 3.272

6.  Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

Authors:  Thom Vreven; Brian G Pierce; Tyler M Borrman; Zhiping Weng
Journal:  Proteins       Date:  2016-10-24

7.  Predicting protein-DNA interactions by full search computational docking.

Authors:  Victoria A Roberts; Michael E Pique; Lynn F Ten Eyck; Sheng Li
Journal:  Proteins       Date:  2013-10-18

8.  Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases.

Authors:  Daniele Dell'orco; Pier Giuseppe De Benedetti
Journal:  J Comput Aided Mol Des       Date:  2008-01-23       Impact factor: 3.686

9.  Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase.

Authors:  Victoria A Roberts; Michael E Pique; Simon Hsu; Sheng Li; Geir Slupphaug; Robert P Rambo; Jonathan W Jamison; Tong Liu; Jun H Lee; John A Tainer; Lynn F Ten Eyck; Virgil L Woods
Journal:  Nucleic Acids Res       Date:  2012-04-06       Impact factor: 16.971

Review 10.  Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.

Authors:  Francesca Fanelli; Pier G De Benedetti
Journal:  J Comput Aided Mol Des       Date:  2006-09-29       Impact factor: 4.179
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