(Q37148484)

18 August 2017

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins (English)

1 reference

18 August 2017

Shandar Ahmad

2

0 references

M Michael Gromiha

series ordinal

3

object named as

M Michael Gromiha

1 reference

18 August 2017

R Nagarajan

1

1 reference

PMC publication ID

3763535

18 August 2017

language of work or name

English

0 references

publication date

20 June 2013

1 reference

18 August 2017

Nucleic Acids Research

1 reference

18 August 2017

41

1 reference

18 August 2017

16

1 reference

18 August 2017

7606-7614

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

18 August 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

A new method for evaluating the specificity of indirect readout in protein-DNA recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

The Protein Data Bank at 40: reflecting on the past to prepare for the future

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Recognition of methylated DNA through methyl-CpG binding domain proteins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Reorganizing the protein space at the Universal Protein Resource (UniProt)

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Dynamic protein–DNA recognition: beyond what can be seen

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Physics of protein-DNA interactions: mechanisms of facilitated target search

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

The Protein-DNA Interface database

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

The role of DNA shape in protein-DNA recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Prediction of DNA-binding residues from protein sequence information using random forests

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Prediction of DNA-binding residues from sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Predicting DNA-binding sites of proteins from amino acid sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Protein-DNA recognition patterns and predictions.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

PSSM-based prediction of DNA binding sites in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Structural analysis of conserved base pairs in protein-DNA complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Structure-based prediction of DNA target sites by regulatory proteins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

SCOP: a structural classification of proteins database for the investigation of sequences and structures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

PRONUC: a software package for the analysis of protein and nucleic acid sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Mechanism of DNA recognition by the restriction enzyme EcoRV.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

NAPS: a residue-level nucleic acid-binding prediction server

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Energetics of protein-DNA interactions

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Protein-DNA interactions: A structural analysis

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Structural features of protein-nucleic acid recognition sites

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

A role for CH...O interactions in protein-DNA recognition

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Importance of DNA stiffness in protein-DNA binding specificity

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Systematic Classification and Analysis of Themes in Protein−DNA Recognition

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Design of accurate predictors for DNA-binding sites in proteins using hybrid SVM-PSSM method.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Cation-pi/H-bond stair motifs at protein-DNA interfaces

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Thermodynamic database for protein-nucleic acid interactions (ProNIT).

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Protein secondary structure prediction in different structural classes

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

The role of DNA bending in Cro protein-DNA interactions

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3763535

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

3 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT544

Influence of cation–π interactions in protein–DNA complexes

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT544

Classification of Protein-DNA Complexes Based on Structural Descriptors

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT544

Scoring function based approach for locating binding sites and understanding recognition mechanism of protein-DNA complexes

21 January 2018

1 reference

12 December 2020

Electrostatic interactions in biological DNA-related systems

1 reference

12 December 2020

Protein-DNA recognition triggered by a DNA conformational switch

1 reference

12 December 2020

Influence of DNA stiffness in protein-DNA recognition

1 reference

12 December 2020

Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?

1 reference

12 December 2020

Contribution of cation-pi interactions to the stability of protein-DNA complexes

1 reference

12 December 2020

A simple probabilistic scoring method for protein domain identification

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKT544

1 reference

18 August 2017

1 reference

PMC publication ID

3763535

18 August 2017

PubMed publication ID

23788679

1 reference

PMC publication ID

3763535