Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential (Q24801775)

1

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Fenglou Mao

2

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Jun-tao Guo

3

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Bo Yan

4

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Peng Wang

5

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Youxing Qu

6

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Ying Xu

Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage

7

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language of work or name

English

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publication date

2005

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published in

Nucleic Acids Research

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volume

33

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issue

2

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page(s)

546-58

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cites work

1 reference

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DNA binding sites: representation and discovery

7 April 2017

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In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence

7 April 2017

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

7 April 2017

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Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

7 April 2017

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Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

7 April 2017

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9 May 2017

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A biophysical approach to transcription factor binding site discovery

28 September 2017

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Gibbs Recursive Sampler: finding transcription factor binding sites

28 September 2017

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Additivity in protein-DNA interactions: how good an approximation is it?

28 September 2017

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

28 September 2017

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Finding motifs in the twilight zone

28 September 2017

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Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees

28 September 2017

1 reference

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Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

28 September 2017

1 reference

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Bending of DNA by asymmetric charge neutralization: all-atom energy simulations

28 September 2017

1 reference

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The Protein Data Bank: unifying the archive

28 September 2017

1 reference

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

28 September 2017

1 reference

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

28 September 2017

1 reference

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

28 September 2017

1 reference

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

28 September 2017

1 reference

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How to derive a protein folding potential? A new approach to an old problem

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions

28 September 2017

1 reference

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Length-encoded multiplex binding site determination: application to zinc finger proteins

28 September 2017

1 reference

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Subtle motifs: defining the limits of motif finding algorithms

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

An efficient computational method for globally optimal threading.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Protein-DNA interaction. No code for recognition

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Identifying transcription factor binding sites through Markov chain optimization

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Finding weak motifs in DNA sequences

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

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

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

A structure-based approach for prediction of protein binding sites in gene upstream regions

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Flexing and folding double helical DNA

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=548349

Potential of mean force for protein-protein interaction studies

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15673715

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

B-DNA twisting correlates with base-pair morphology.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15673715

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

DNA stretching and compression: large-scale simulations of double helical structures

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15673715

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKI204

1 reference

1 reference

1 reference

PubMed publication ID

15673715

1 reference