(Q34996988)

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Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains

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Europe PubMed Central

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5 August 2017

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains (English)

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Europe PubMed Central

PubMed publication ID

5 August 2017

Harold A. Scheraga

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Harold A Scheraga

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Europe PubMed Central

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5 August 2017

2

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Adam Liwo

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5 August 2017

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Mariusz Makowski

1

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5 August 2017

Emil Sobolewski

3

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5 August 2017

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publication date

18 April 2011

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5 August 2017

Journal of Physical Chemistry B

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5 August 2017

115

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Europe PubMed Central

PubMed publication ID

5 August 2017

19

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Europe PubMed Central

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5 August 2017

6119-6129

1 reference

Europe PubMed Central

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5 August 2017

Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3099398

8 July 2018

Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit.

1 reference

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8 July 2018

An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

1 reference

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Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field

1 reference

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8 July 2018

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3099398

8 July 2018

Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model.

1 reference

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8 July 2018

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3099398

8 July 2018

Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3099398

8 July 2018

Energetic and entropic contributions to the interactions between like-charged groups in cationic peptides: A molecular dynamics simulation study

1 reference

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8 July 2018

Generalized born models of macromolecular solvation effects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3099398

8 July 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=3099398

8 July 2018

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment

1 reference

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Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force.

1 reference

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26 October 2018

Statistical potentials extracted from protein structures: how accurate are they?

1 reference

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26 October 2018

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/21500792

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Contribution of unusual arginine-arginine short-range interactions to stabilization and recognition in proteins

1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Potentials of mean force between ionizable amino acid side chains in water

1 reference

https://pubmed.ncbi.nlm.nih.gov/21500792

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains

1 reference

https://pubmed.ncbi.nlm.nih.gov/21500792

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model

1 reference

https://pubmed.ncbi.nlm.nih.gov/21500792

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I.

1 reference

https://pubmed.ncbi.nlm.nih.gov/21500792

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP111258P

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

5 August 2017

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