Gaussian-mixture umbrella sampling (Q33590763)

28 July 2017

Gaussian-mixture umbrella sampling (English)

1 reference

28 July 2017

3

Martin Karplus

1 reference

28 July 2017

Paul Maragakis

1

1 reference

PubMed ID

19284746

28 July 2017

Arjan van der Vaart

series ordinal

2

1 reference

PubMed ID

19284746

28 July 2017

language of work or name

English

0 references

publication date

1 April 2009

1 reference

Journal of Physical Chemistry B

28 July 2017

1 reference

28 July 2017

113

1 reference

28 July 2017

14

1 reference

28 July 2017

4664-4673

1 reference

Statistically optimal analysis of samples from multiple equilibrium states

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Diffusive reaction dynamics on invariant free energy profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Finding transition pathways using the string method with swarms of trajectories

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

A bias-exchange approach to protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

The experimental survey of protein-folding energy landscapes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Hidden complexity of free energy surfaces for peptide (protein) folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Escaping free-energy minima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Conformational substates in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

A differential fluctuation theorem

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Coarse master equations for peptide folding dynamics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Temperature weighted histogram analysis method, replica exchange, and transition paths.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Optimal estimates of free energies from multistate nonequilibrium work data.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Equilibrium Free Energies from Nonequilibrium Metadynamics

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2806548

Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods

31 October 2018

1 reference

12 December 2020

Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide

1 reference

12 December 2020

Optimized free energies from bidirectional single-molecule force spectroscopy

1 reference

12 December 2020

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Conformational analysis of a stereochemically complete set of cis-enediol peptide analogues

1 reference

12 December 2020

Predicting slow structural transitions in macromolecular systems: Conformational flooding

1 reference

12 December 2020

Microfolding: Conformational probability map for the alanine dipeptide in water from molecular dynamics simulations

1 reference

12 December 2020

Simulation of activation free energies in molecular systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

The Selection of Prior Distributions by Formal Rules

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

Replica-exchange molecular dynamics method for protein folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

Simulated Tempering: A New Monte Carlo Scheme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

String method in collective variables: minimum free energy paths and isocommittor surfaces.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

An Essay towards Solving a Problem in the Doctrine of Chances. By the Late Rev. Mr. Bayes, F. R. S. Communicated by Mr. Price, in a Letter to John Canton, A. M. F. R. S

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP808381S

Identifiers

DOI

10.1021/JP808381S

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

PubMed ID

19284746