(Q41889863)

English

Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters

scientific article published on 27 May 2012

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters (English)

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

author name string

Sucharita Dey

1

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Arumay Pal

2

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Mainak Guharoy

3

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Shrihari Sonavane

4

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Pinak Chakrabarti

5

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

language of work or name

1 reference

based on heuristic

inferred from title

publication date

27 May 2012

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Nucleic Acids Research

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

40

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

15

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

7150-7161

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

Prediction of dinucleotide-specific RNA-binding sites in proteins

1 reference

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1 reference

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5 June 2018

Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures

1 reference

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5 June 2018

Predicting nucleic acid binding interfaces from structural models of proteins

1 reference

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From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces

1 reference

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5 June 2018

MetaDBSite: a meta approach to improve protein DNA-binding sites prediction

1 reference

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Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

1 reference

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Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

1 reference

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Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

1 reference

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5 June 2018

Insights into protein-DNA interactions through structure network analysis

1 reference

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A protein-DNA docking benchmark

1 reference

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5 June 2018

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

1 reference

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5 June 2018

Prediction of DNA-binding residues from sequence

1 reference

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5 June 2018

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

1 reference

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5 June 2018

DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins

1 reference

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5 June 2018

BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences.

1 reference

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5 June 2018

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

1 reference

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5 June 2018

Protein-DNA binding specificity predictions with structural models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3424558

5 June 2018

Conservation and relative importance of residues across protein-protein interfaces

1 reference

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5 June 2018

Protein-DNA recognition patterns and predictions.

1 reference

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5 June 2018

PSSM-based prediction of DNA binding sites in proteins

1 reference

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Moment-based prediction of DNA-binding proteins

1 reference

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Data mining in bioinformatics using Weka

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1 reference

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Conserved residue clustering and protein structure prediction.

1 reference

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The Protein Data Bank

1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

1 reference

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Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity

1 reference

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Rapid comparison of protein structures

1 reference

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Dissecting protein-protein recognition sites

1 reference

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Dissection, residue conservation, and structural classification of protein-DNA interfaces

1 reference

https://pubmed.ncbi.nlm.nih.gov/22641851

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based on heuristic

inferred from PubMed ID database lookup

The subunit interfaces of weakly associated homodimeric proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/22641851

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inferred from PubMed ID database lookup

Do water molecules mediate protein-DNA recognition?

1 reference

https://pubmed.ncbi.nlm.nih.gov/22641851

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1 reference

https://pubmed.ncbi.nlm.nih.gov/22641851

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Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

1 reference

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12 December 2020

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Identifiers

10.1093/NAR/GKS405

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

ResearchGate publication ID

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