(Q35574706)

English

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

scientific article published on August 2005

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scholarly article

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Europe PubMed Central

PubMed publication ID

8 August 2017

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties (English)

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

author name string

Xianfeng Li

1

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

Sergio A Hassan

2

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

Ernest L Mehler

3

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

language of work or name

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publication date

1 August 2005

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

60

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

3

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

464-484

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

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

1 reference

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Exploring peptide energy landscapes: a test of force fields and implicit solvent models.

1 reference

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12 July 2018

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

1 reference

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12 July 2018

The contribution of polar group burial to protein stability is strongly context-dependent

1 reference

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12 July 2018

Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.

1 reference

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12 July 2018

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.

1 reference

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12 July 2018

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

1 reference

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12 July 2018

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

1 reference

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12 July 2018

Molecular dynamics simulations of biomolecules

1 reference

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12 July 2018

Probing protein electrostatics with a synthetic fluorescent amino acid.

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12 July 2018

Drying-induced hydrophobic polymer collapse

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12 July 2018

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

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12 July 2018

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

1 reference

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12 July 2018

Tyrosine hydrogen bonds make a large contribution to protein stability

1 reference

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12 July 2018

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

1 reference

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12 July 2018

Macromolecular electrostatics: continuum models and their growing pains

1 reference

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12 July 2018

Autoionization in liquid water

1 reference

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12 July 2018

Polar group burial contributes more to protein stability than nonpolar group burial

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Molecular dynamics simulation of nucleic acids

1 reference

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12 July 2018

Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Effective energy function for proteins in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Unified Approach for Molecular Dynamics and Density-Functional Theory

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Microscopic pKa values of Escherichia coli thioredoxin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

A molecular dynamics simulation study of segment B1 of protein G.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Adding backbone to protein folding: why proteins are polypeptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Hydrogen bonding stabilizes globular proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Investigation of the backbone dynamics of the IgG-binding domain of streptococcal protein G by heteronuclear two-dimensional 1H-15N nuclear magnetic resonance spectroscopy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

A sampling problem in molecular dynamics simulations of macromolecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Folding of Protein G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure Elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its G36S mutant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Hydrogen bonding in globular proteins

1 reference

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12 July 2018

Calculations of electrostatic interactions in biological systems and in solutions

1 reference

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12 July 2018

Hydrophobic bonding and accessible surface area in proteins

1 reference

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12 July 2018

Hydrogen bonding and biological specificity analysed by protein engineering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Stabilization of charges on isolated ionic groups sequestered in proteins by polarized peptide units

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Structure of ubiquitin refined at 1.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Accurate simulation of protein dynamics in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

Structure of form III crystals of bovine pancreatic trypsin inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

The meaning of hydrophobicity

1 reference

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12 July 2018

Hydrophobicity of amino acid subgroups in proteins

1 reference

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12 July 2018

Electrostatic interactions in macromolecules: theory and applications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

12 July 2018

A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G

1 reference

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12 July 2018

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

1 reference

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12 July 2018

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

1 reference

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12 July 2018

Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme

1 reference

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12 July 2018

Electrostatic Energy and Macromolecular Function

1 reference

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12 July 2018

A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.

1 reference

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12 July 2018

Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G.

1 reference

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Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

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The determinants of carboxyl pKa values in turkey ovomucoid third domain

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A semi-implicit solvent model for the simulation of peptides and proteins.

1 reference

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26 September 2018

Improved treatment of the protein backbone in empirical force fields.

1 reference

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Structure, dynamics, and energetics of water at the surface of a small globular protein: A molecular dynamics simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

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Key issues in the computational simulation of GPCR function: representation of loop domains.

1 reference

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An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

26 September 2018

Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

26 September 2018

Hydrophobicity: two faces of water.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

26 September 2018

Structural dependencies of interresidue scalar coupling (h3)J(NC') and donor (1)H chemical shifts in the hydrogen bonding regions of proteins

1 reference

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26 September 2018

Making a network of hydrophobic clusters

1 reference

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26 September 2018

A critical analysis of continuum electrostatics: the screened Coulomb potential--implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins

1 reference

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26 September 2018

Characterization of pKa values and titration shifts in the cytotoxic ribonuclease alpha-sarcin by NMR. Relationship between electrostatic interactions, structure, and catalytic function.

1 reference

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26 September 2018

Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

26 September 2018

Electrostatic effects in macromolecules: fundamental concepts and practical modeling

1 reference

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26 September 2018

Simulations of the structural and dynamical properties of denatured proteins: the "molten coil" state of bovine pancreatic trypsin inhibitor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1764639

26 September 2018

Dielectric Dispersion of Crystalline Powders of Amino Acids, Peptides, and Proteins1

1 reference

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26 September 2018

The Prediction of Protein pKa's Using QM/MM: The pKaof Lysine 55 in Turkey Ovomucoid Third Domain

1 reference

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Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

1 reference

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15 November 2018

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1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Determinants of backbone dynamics in native BPTI: cooperative influence of the 14-38 disulfide and the Tyr35 side-chain

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

De novo design and structural analysis of a model beta-hairpin peptide system

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Buried, charged, non-ion-paired aspartic acid 76 contributes favorably to the conformational stability of ribonuclease T1

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effect of cysteine-25 on the ionization of histidine-159 in papain as determined by proton nuclear magnetic resonance spectroscopy. Evidence for a his-159--Cys-25 ion pair and its possible role in catalysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Further observations on the electrical properties of hemoglobin-bound water

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dielectric relaxation spectra of water adsorbed on lysozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Conformational equilibria in -and -chymotrypsin. The energetics and importance of the salt bridge

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluating contribution of hydrogen bonding and hydrophobic bonding to protein folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Computer simulation of local order in condensed phases of silicon

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Ionization constants of two active-site lysyl epsilon-amino groups of ribulosebisphosphate carboxylase/oxygenase

1 reference

https://pubmed.ncbi.nlm.nih.gov/15959866

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/PROT.20470

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

8 August 2017

ResearchGate publication ID

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