(Q40242616)

18 September 2017

Protocol for MM/PBSA molecular dynamics simulations of proteins (English)

1 reference

18 September 2017

Federico Fogolari

1

0 references

author name string

Alessandro Brigo

series ordinal

2

1 reference

PMCID

1303073

18 September 2017

Henriette Molinari

series ordinal

3

1 reference

PMCID

1303073

18 September 2017

language of work or name

English

0 references

publication date

1 July 2003

1 reference

18 September 2017

1 reference

18 September 2017

85

1 reference

18 September 2017

1

1 reference

18 September 2017

159-166

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

22 September 2017

Implicit solvent models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

What are the dielectric "constants" of proteins and how to validate electrostatic models?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Macromolecular electrostatics: continuum models and their growing pains

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

22 September 2017

Polarizable force fields

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

NMR structural determination of viscotoxin A3 from Viscum album L

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Effective energy function for proteins in solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Biomolecular electrostatics with the linearized Poisson-Boltzmann equation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Classical electrostatics in biology and chemistry

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Solvation energy in protein folding and binding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Treatment of electrostatic effects in macromolecular modeling

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Electrostatic effects in proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

The hydrophobic effect and the organization of living matter

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Future directions for combining molecular and continuum models in protein simulations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Prediction of pH-dependent properties of proteins

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Accelerated Poisson-Boltzmann calculations for static and dynamic systems

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Molecular mechanics and dynamics of biomolecules using a solvent continuum model.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303073

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

4 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

On the variational approach to Poisson–Boltzmann free energies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Simulation of activation free energies in molecular systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Phosphorylation stabilizes the N-termini of alpha-helices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Semianalytical treatment of solvation for molecular mechanics and dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

A smooth particle mesh Ewald method

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2803%2974462-2

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(03)74462-2

1 reference

18 September 2017

1 reference

18 September 2017

1 reference

PMCID

1303073