(Q38698407)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

title

Advances in free-energy-based simulations of protein folding and ligand binding (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

0 references

Joseph A Morrone

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

Carlos Simmerling

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

publication date

7 January 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

Current Opinion in Structural Biology

5 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

volume

36

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

page(s)

25-31

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

5 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Accelerating molecular simulations of proteins using Bayesian inference on weak information.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Mapping fast protein folding with multiple-site fluorescent probes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Improved Generalized Born Solvent Model Parameters for Protein Simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Computational studies of protein aggregation: methods and applications

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

A structural and energetic model for the slow-onset inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Phosphate release coupled to rotary motion of F1-ATPase

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

How hydrophobic drying forces impact the kinetics of molecular recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Funnel metadynamics as accurate binding free-energy method

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Microsecond folding experiments and simulations: a match is made

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Residue-specific α-helix propensities from molecular simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Systematic validation of protein force fields against experimental data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

How fast-folding proteins fold

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Pathway and mechanism of drug binding to G-protein-coupled receptors.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Drug-target residence time: critical information for lead optimization.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Context-independent, temperature-dependent helical propensities for amino acid residues

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Statistically optimal analysis of samples from multiple equilibrium states

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

COMPUTING: Screen Savers of the World Unite!

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Predicting absolute ligand binding free energies to a simple model site

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Development and validation of a modular, extensible docking program: DOCK 5.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Drug-target residence time and its implications for lead optimization

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Calculation of absolute protein-ligand binding free energy from computer simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Improved protein-ligand docking using GOLD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Dynamics of folded proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

How does a drug molecule find its target binding site?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

New force field on modeling intrinsically disordered proteins.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Scaling of folding times with protein size

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

3 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4785060

Visualizing the Induced Binding of SH2-Phosphopeptide

3 December 2018

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study

1 reference

12 December 2020

Free energy calculations by computer simulation

1 reference

12 December 2020

Balance between α and β Structures in Ab Initio Protein Folding

1 reference

12 December 2020

10.1016/J.SBI.2015.12.002

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

PubMed publication ID

26773233

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26773233%20AND%20SRC:MED&resulttype=core&format=json