(Q30410742)

14 September 2017

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

1 reference

14 September 2017

Yi Xiong

1

0 references

Junfeng Xia

object named as

Junfeng Xia

series ordinal

2

0 references

author name string

Wen Zhang

series ordinal

3

1 reference

14 September 2017

Juan Liu

series ordinal

4

1 reference

14 September 2017

language of work or name

English

0 references

publication date

8 December 2011

1 reference

14 September 2017

1 reference

14 September 2017

6

1 reference

14 September 2017

12

1 reference

14 September 2017

e28440

1 reference

Creative Commons Attribution 4.0 International

14 September 2017

start time

8 December 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature

1 reference

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

20 June 2018

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Novel feature for catalytic protein residues reflecting interactions with other residues

20 June 2018

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Exploiting structural and topological information to improve prediction of RNA-protein binding sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Identification of DNA-binding proteins using structural, electrostatic and evolutionary features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Insights into protein-DNA interactions through structure network analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Prediction of DNA-binding residues from sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

How accurate and statistically robust are catalytic site predictions based on closeness centrality?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Predicting DNA-binding sites of proteins from amino acid sequence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

PSSM-based prediction of DNA binding sites in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Annotating nucleic acid-binding function based on protein structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Testing water-mediated DNA recognition by the Hin recombinase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

An overview of the structures of protein-DNA complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Protein secondary structure prediction based on position-specific scoring matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Structural features of protein-nucleic acid recognition sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3234263

Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach.

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

An accurate feature-based method for identifying DNA-binding residues on protein surfaces.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Understanding the recognition mechanism of protein-RNA complexes using energy based approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Prediction of protein-protein interaction sites using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

Accurate sequence-based prediction of catalytic residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028440

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Small-world network approach to identify key residues in protein-protein interaction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifying folding nucleus based on residue contact networks of proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22174808

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0028440

1 reference

14 September 2017

0 references

1 reference

14 September 2017

PubMed publication ID

22174808

1 reference