Literature DB >> 15613393

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces.

Yuko Tsuchiya1, Kengo Kinoshita, Haruki Nakamura.   

Abstract

UNLABELLED: PreDs is a WWW server that predicts the dsDNA-binding sites on protein molecular surfaces generated from the atomic coordinates in a PDB format. The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer. AVAILABILITY: PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/ CONTACT: kino@ims.u-tokyo.ac.jp.

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Year:  2004        PMID： 15613393     DOI： 10.1093/bioinformatics/bti232

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  25 in total

1.  Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants.

Authors:  Bryan F Shaw; Grégory F Schneider; Haribabu Arthanari; Max Narovlyansky; Demetri Moustakas; Armando Durazo; Gerhard Wagner; George M Whitesides
Journal:  J Am Chem Soc       Date:  2011-10-13       Impact factor: 15.419

Review 2.  DNA-protein interactions: methods for detection and analysis.

Authors:  Bipasha Dey; Sameer Thukral; Shruti Krishnan; Mainak Chakrobarty; Sahil Gupta; Chanchal Manghani; Vibha Rani
Journal:  Mol Cell Biochem       Date:  2012-03-08       Impact factor: 3.396

3.  Homology modeling of human Toll-like receptors TLR7, 8, and 9 ligand-binding domains.

Authors:  Tiandi Wei; Jing Gong; Ferdinand Jamitzky; Wolfgang M Heckl; Robert W Stark; Shaila C Rössle
Journal:  Protein Sci       Date:  2009-08       Impact factor: 6.725

4.  Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.

Authors:  Wen Hu; Liu Qin; Menglong Li; Xuemei Pu; Yanzhi Guo
Journal:  J Comput Aided Mol Des       Date:  2018-11-26       Impact factor: 3.686

5.  Disruption and formation of surface salt bridges are coupled to DNA binding by the integration host factor: a computational analysis.

Authors:  L Ma; N K Sundlass; R T Raines; Q Cui
Journal:  Biochemistry       Date:  2010-12-15       Impact factor: 3.162

6.  Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes.

Authors:  Kyle E Kemege; John M Hickey; Scott Lovell; Kevin P Battaile; Yang Zhang; P Scott Hefty
Journal:  J Bacteriol       Date:  2011-09-30       Impact factor: 3.490

7.  Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity.

Authors:  Ching-I A Wang; Gregor Guncar; Jade K Forwood; Trazel Teh; Ann-Maree Catanzariti; Gregory J Lawrence; Fionna E Loughlin; Joel P Mackay; Horst Joachim Schirra; Peter A Anderson; Jeffrey G Ellis; Peter N Dodds; Bostjan Kobe
Journal:  Plant Cell       Date:  2007-09-14       Impact factor: 11.277

8.  DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.

Authors:  Pemra Ozbek; Seren Soner; Burak Erman; Turkan Haliloglu
Journal:  Nucleic Acids Res       Date:  2010-05-16       Impact factor: 16.971

9.  HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.

Authors:  Agnieszka Obarska-Kosinska; James E Taylor; Philip Callow; Jerzy Orlowski; Janusz M Bujnicki; G Geoff Kneale
Journal:  J Mol Biol       Date:  2007-11-17       Impact factor: 5.469

10.  DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.

Authors:  Samuel Godfrey Hendrix; Kuan Y Chang; Zeezoo Ryu; Zhong-Ru Xie
Journal:  Int J Mol Sci       Date:  2021-05-24       Impact factor: 5.923
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