Mapping transiently formed and sparsely populated conformations on a complex energy landscape (Q41316433)

29 September 2017

Mapping transiently formed and sparsely populated conformations on a complex energy landscape (English)

1 reference

29 September 2017

1 reference

2

1 reference

PMCID

5050026

29 September 2017

Kresten Lindorff-Larsen

series ordinal

3

1 reference

29 September 2017

1

Yong Wang

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language of work or name

English

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publication date

23 August 2016

1 reference

29 September 2017

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29 September 2017

5

1 reference

Replica-Averaged Metadynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Role of water and steric constraints in the kinetics of cavity-ligand unbinding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Homologous ligands accommodated by discrete conformations of a buried cavity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

ALMOST: an all atom molecular simulation toolkit for protein structure determination.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Combining experiments and simulations using the maximum entropy principle

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Studying "invisible" excited protein states in slow exchange with a major state conformation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Exploration of multi-state conformational dynamics and underlying global functional landscape of maltose binding protein

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Solution structure of a minor and transiently formed state of a T4 lysozyme mutant

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

A self-learning algorithm for biased molecular dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Improved side-chain torsion potentials for the Amber ff99SB protein force field

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Hidden alternative structures of proline isomerase essential for catalysis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

NMR spectroscopy brings invisible protein states into focus

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Canonical sampling through velocity rescaling

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Application of a Theory of Enzyme Specificity to Protein Synthesis

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Quaternary structure of hemoglobin in solution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Escaping free-energy minima

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Studying excited states of proteins by NMR spectroscopy.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Theory of protein folding: the energy landscape perspective

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

From metadynamics to dynamics.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

How robust are protein folding simulations with respect to force field parameterization?

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

On the Use of Experimental Observations to Bias Simulated Ensembles

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Metadynamics with Adaptive Gaussians.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Tackling sampling challenges in biomolecular simulations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Well-tempered metadynamics converges asymptotically.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

From A to B in free energy space.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5050026

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

19 August 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.17505

Access of ligands to cavities within the core of a protein is rapid

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.17505

Conformational Changes and Free Energies in a Proline Isomerase

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.17505

The role of water in host-guest interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.17505

Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.7554%2FELIFE.17505

Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states

21 January 2018

1 reference

12 December 2020

Enhanced sampling in the well-tempered ensemble

1 reference

12 December 2020

Exploring the free energy surfaces of clusters using reconnaissance metadynamics

1 reference

12 December 2020

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

1 reference

12 December 2020

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

1 reference

12 December 2020

Atomistic picture of conformational exchange in a T4 lysozyme cavity mutant: an experiment-guided molecular dynamics study† †Electronic supplementary information (ESI) available: Additional figures, a table and details regarding the NMR experiments,

1 reference

12 December 2020

Identifiers

DOI

10.7554/ELIFE.17505

1 reference

29 September 2017

1 reference

29 September 2017

1 reference

PMCID

5050026