(Q42554397)

English

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

scientific article published on August 2009

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

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

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

protein function prediction

0 references

2

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

4

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

object named as

Beisi Xu

1

0 references

author name string

Haojun Liang

3

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

language of work or name

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publication date

1 August 2009

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

76

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

3

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

718-730

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Energetics of protein-DNA interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Indirect readout: detection of optimized subsequences and calculation of relative binding affinities using different DNA elastic potentials.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

What is a desirable statistical energy function for proteins and how can it be obtained?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

In quest of an empirical potential for protein structure prediction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 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=2743280

28 May 2018

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Looking into DNA recognition: zinc finger binding specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Toward an atomistic model for predicting transcription-factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Force fields for protein simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

PISCES: a protein sequence culling server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Development of unified statistical potentials describing protein-protein interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

A structure-based method for derivation of all-atom potentials for protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

28 May 2018

Specific interactions for ab initio folding of protein terminal regions with secondary structures.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Weight matrices for protein-DNA binding sites from a single co-crystal structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

A simple physical model for the prediction and design of protein-DNA interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Analyzing protein-DNA recognition mechanisms.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

16 August 2018

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2743280

1 December 2018

Specificity in Protein–DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI

1 reference

https://pubmed.ncbi.nlm.nih.gov/19274740

12 December 2020

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Identifiers

10.1002/PROT.22384

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

2 November 2017

ResearchGate publication ID

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