(Q41652026)

6 October 2017

Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method (English)

1 reference

6 October 2017

2

1 reference

6 October 2017

Harianto Tjong

1

1 reference

6 October 2017

6 September 2008

1 reference

Journal of Chemical Theory and Computation

6 October 2017

1 reference

6 October 2017

4

1 reference

6 October 2017

10

1 reference

6 October 2017

1733-1744

1 reference

Prediction of protein solubility from calculation of transfer free energy

6 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Protein stability prediction: a Poisson-Boltzmann approach

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Electrostatic rate enhancement and transient complex of protein-protein association

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Energy landscape and transition state of protein-protein association

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Comparison of multiple Amber force fields and development of improved protein backbone parameters

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Electrostatic contribution to the binding stability of protein-protein complexes.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Interactions of macromolecules with salt ions: an electrostatic theory for the Hofmeister effect

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Improving implicit solvent simulations: a Poisson-centric view

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Recent advances in the development and application of implicit solvent models in biomolecule simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Electrostatics of nanosystems: application to microtubules and the ribosome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Generalized born models of macromolecular solvation effects

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Structure of Cdc42 in complex with the GTPase-binding domain of the 'Wiskott-Aldrich syndrome' protein

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

GBr(6): a parameterization-free, accurate, analytical generalized born method.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Effects of pH, salt, and macromolecular crowding on the stability of FK506-binding protein: an integrated experimental and theoretical study

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Constant pH molecular dynamics in generalized Born implicit solvent

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

Do electrostatic interactions destabilize protein-nucleic acid binding?

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3587178

An electrostatic steering mechanism of Cdc42 recognition by Wiskott-Aldrich syndrome proteins

4 November 2018

1 reference

12 December 2020

Prediction of Protein-Protein Association Rates from a Transition-State Theory

1 reference

12 December 2020

Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation

1 reference

12 December 2020

Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT8001656

1 reference

6 October 2017

1 reference

PMC publication ID

3587178

6 October 2017

PubMed publication ID

23468599

1 reference

PMC publication ID

3587178