Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. (Q51641693)

8 April 2018

http://europepmc.org/abstract/MED/11913374

title

Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. (English)

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8 April 2018

http://europepmc.org/abstract/MED/11913374

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Jayaram B

1

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8 April 2018

http://europepmc.org/abstract/MED/11913374

McConnell K

2

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http://europepmc.org/abstract/MED/11913374

Dixit SB

3

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http://europepmc.org/abstract/MED/11913374

Das A

4

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http://europepmc.org/abstract/MED/11913374

Beveridge DL

5

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http://europepmc.org/abstract/MED/11913374

publication date

1 January 2002

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8 April 2018

http://europepmc.org/abstract/MED/11913374

published in

Journal of Computational Chemistry

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8 April 2018

http://europepmc.org/abstract/MED/11913374

volume

23

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http://europepmc.org/abstract/MED/11913374

issue

1

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page(s)

1-14

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8 April 2018

http://europepmc.org/abstract/MED/11913374

cites work

Protein-DNA interaction. No code for recognition

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

A structural taxonomy of DNA-binding domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Transcription factors: structural families and principles of DNA recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

DNA recognition code of transcription factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Eukaryotic transcription factor-DNA complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

DNA curvature and deformation in protein-DNA complexes: a step in the right direction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Structures of larger proteins, protein-ligand and protein-DNA complexes by multi-dimensional heteronuclear NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

On the specificity of DNA-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Structural features of protein-nucleic acid recognition sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Protein-protein recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Computational methods to predict binding free energy in ligand-receptor complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Poisson-Boltzmann analysis of the lambda repressor-operator interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Crystal structure of trp repressor/operator complex at atomic resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The Protein Data Bank: a computer-based archival file for macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Generalized born models of macromolecular solvation effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The interpretation of protein structures: Estimation of static accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Coupling of local folding to site-specific binding of proteins to DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Sequence-specific DNA-binding dominated by dehydration

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

On the magnitude of the electrostatic contribution to ligand-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Sequence-dependent dynamics of TATA-Box binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Free energy via molecular simulation: applications to chemical and biomolecular systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Protein-DNA recognition: new perspectives and underlying themes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

The role of water in protein-DNA interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Physical basis of a protein-DNA recognition code

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Role of hydrogen bonds in protein-DNA recognition: a comparison of generalized born and finite difference Poisson-Boltzmann solvation treatments

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

Modeling DNA deformations induced by minor groove binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

DNA curvature and phosphate neutralization: an important aspect of specific protein binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FJCC.10009

21 January 2018

Identifiers

DOI

10.1002/JCC.10009

1 reference

8 April 2018

http://europepmc.org/abstract/MED/11913374

DBLP publication ID

journals/jcc/JayaramMDDB02

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

8 April 2018