(Q36710407)

15 August 2017

Spectral gap optimization of order parameters for sampling complex molecular systems (English)

1 reference

15 August 2017

Pratyush Tiwary

1

1 reference

15 August 2017

B J Berne

series ordinal

2

1 reference

15 August 2017

language of work or name

English

0 references

publication date

29 February 2016

1 reference

15 August 2017

6

1 reference

Proceedings of the National Academy of Sciences of the United States of America

inferred from page(s)

published in

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15 August 2017

113

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15 August 2017

11

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15 August 2017

2839-2844

1 reference

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint.

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Metainference: A Bayesian inference method for heterogeneous systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Locating landmarks on high-dimensional free energy surfaces

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Time scale separation leads to position-dependent diffusion along a slow coordinate

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Dewetting and hydrophobic interaction in physical and biological systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Canonical sampling through velocity rescaling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Drug-target residence time and its implications for lead optimization

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Reaction coordinates and rates from transition paths

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Escaping free-energy minima

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Unified Approach for Molecular Dynamics and Density-Functional Theory

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

From metadynamics to dynamics.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Metadynamics with Adaptive Gaussians.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

A time-independent free energy estimator for metadynamics.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Parameter space compression underlies emergent theories and predictive models

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Identification of slow molecular order parameters for Markov model construction

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Determination of reaction coordinates via locally scaled diffusion map.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Adaptive biasing force method for scalar and vector free energy calculations

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

From A to B in free energy space.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Obtaining reaction coordinates by likelihood maximization.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Automatic method for identifying reaction coordinates in complex systems.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Computing time scales from reaction coordinates by milestoning.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801247

Numerical calculation of the rate of homogeneous gas–liquid nucleation in a Lennard-Jones system

5 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Information Theory and Statistical Mechanics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple-minima problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

The role of water in host-guest interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1600917113

Well-Tempered Variational Approach to Enhanced Sampling

21 January 2018

1 reference

12 December 2020

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics

1 reference

12 December 2020

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes

1 reference

12 December 2020

Variational approach to enhanced sampling and free energy calculations

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1600917113

1 reference

15 August 2017

0 references

1 reference

0 references

1 reference

15 August 2017

PubMed publication ID

26929365

1 reference