(Q42854093)

8 November 2017

Energetics of protein-DNA interactions (English)

1 reference

8 November 2017

Eugene I. Shakhnovich

series ordinal

3

object named as

Eugene I Shakhnovich

1 reference

8 November 2017

Jason E Donald

1

1 reference

PMCID

1851630

8 November 2017

William W Chen

series ordinal

2

1 reference

PMCID

1851630

8 November 2017

language of work or name

English

0 references

publication date

26 January 2007

1 reference

8 November 2017

Nucleic Acids Research

1 reference

8 November 2017

35

1 reference

8 November 2017

4

1 reference

8 November 2017

1039-1047

1 reference

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

8 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

High-resolution protein folding with a transferable potential

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Protein-DNA binding specificity predictions with structural models

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Lessons from the design of a novel atomic potential for protein folding

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Looking into DNA recognition: zinc finger binding specificity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Toward an atomistic model for predicting transcription-factor binding sites

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Orientational potentials extracted from protein structures improve native fold recognition

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Simplicial edge representation of protein structures and alpha contact potential with confidence measure.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

An overview of the structures of protein-DNA complexes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

27 May 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851630

Statistical mechanics of proteins with "evolutionary selected" sequences

1 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17259221

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17259221

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL1103

1 reference

8 November 2017

1 reference

1 reference

8 November 2017

1 reference

PMCID

1851630