Atomistic modeling of protein-DNA interaction specificity: progress and applications (Q36182638)

12 August 2017

Atomistic modeling of protein-DNA interaction specificity: progress and applications (English)

1 reference

12 August 2017

Limin Angela Liu

1

1 reference

PMCID

3425445

12 August 2017

Philip Bradley

series ordinal

2

1 reference

PMCID

3425445

12 August 2017

language of work or name

1 reference

13 July 2012

1 reference

Current Opinion in Structural Biology

12 August 2017

1 reference

12 August 2017

22

1 reference

12 August 2017

4

1 reference

12 August 2017

397-405

1 reference

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

ParaDock: a flexible non-specific DNA--rigid protein docking algorithm

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Direct inference of protein-DNA interactions using compressed sensing methods

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Towards computational specificity screening of DNA-binding proteins

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Determining the specificity of protein-DNA interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Structure-based DNA-binding prediction and design.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

The Protein-DNA Interface database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Breaking the code of DNA binding specificity of TAL-type III effectors

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

A simple cipher governs DNA recognition by TAL effectors

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

A threading-based method for the prediction of DNA-binding proteins with application to the human genome.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

The role of DNA shape in protein-DNA recognition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

3D-footprint: a database for the structural analysis of protein-DNA complexes.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Prediction of TF target sites based on atomistic models of protein-DNA complexes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Predicting transcription factor specificity with all-atom models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Ab initio prediction of transcription factor binding sites.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Protein-DNA binding specificity predictions with structural models

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

DNA bending: the prevalence of kinkiness and the virtues of normality

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Sequence logos: a new way to display consensus sequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Structural modeling of TAL effector-DNA interactions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

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

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Energetics of protein-DNA interactions

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Structure-based ab initio prediction of transcription factor-binding sites

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3425445

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22796087

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22796087

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.SBI.2012.06.002

1 reference

12 August 2017

1 reference

12 August 2017

1 reference

PMCID

3425445