(Q37480652)

20 August 2017

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides (English)

1 reference

20 August 2017

dimensionality reduction

1 reference

nonlinear dimensionality reduction

inferred from title

1 reference

3

Lydia E Kavraki

1 reference

20 August 2017

2

Cecilia Clementi

1 reference

20 August 2017

Hernán Stamati

1

1 reference

PMCID

2795065

20 August 2017

language of work or name

English

0 references

publication date

1 February 2010

1 reference

20 August 2017

1 reference

20 August 2017

78

1 reference

20 August 2017

2

1 reference

20 August 2017

223-235

1 reference

Replica exchange statistical temperature Monte Carlo

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Recent advances in implicit solvent-based methods for biomolecular simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Coarse-grained models of protein folding: toy models or predictive tools?

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

The MARTINI force field: coarse grained model for biomolecular simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Multiscale modeling of biomolecular systems: in serial and in parallel

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Studies of folding and misfolding using simplified models.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Molecular dynamics and protein function

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Long-timescale simulation methods

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Development and testing of a general amber force field

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Conformational sampling for the impatient

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Minimalist models for protein folding and design

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Molecular dynamics simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Nonlinear dimensionality reduction by locally linear embedding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Reaction coordinates of biomolecular isomerization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom 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=2795065

Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

On the assumptions underlying milestoning

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Optimization methods for finding minimum energy paths.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Illustration of transition path theory on a collection of simple examples.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Automatic method for identifying reaction coordinates in complex systems.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Resolution exchange simulation.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Efficient sampling of protein structures by model hopping.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Improved theoretical description of protein folding kinetics from rotations in the phase space of relevant order parameters.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Role of solvent in determining conformational preferences of alanine dipeptide in water.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

A global geometric framework for nonlinear dimensionality reduction

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2795065

An approximate method in using molecular mechanics simulations to study slow protein conformational changes

3 December 2018

1 reference

12 December 2020

Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules

1 reference

12 December 2020

Minimalist protein model as a diagnostic tool for misfolding and aggregation

1 reference

12 December 2020

Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site

1 reference

12 December 2020

New Monte Carlo technique for studying phase transitions

1 reference

12 December 2020

Adaptive kinetic Monte Carlo for first-principles accelerated dynamics

1 reference

12 December 2020

Geometry of the energy landscape and folding transition in a simple model of a protein

1 reference

12 December 2020

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Understanding protein flexibility through dimensionality reduction

1 reference

12 December 2020

Optimized Monte Carlo data analysis

1 reference

12 December 2020

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22526

1 reference

20 August 2017

1 reference

20 August 2017

1 reference

PMCID

2795065