Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics (Q28689971)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

CHARMM: the biomolecular simulation program

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Development and validation of a genetic algorithm for flexible docking

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Modelling proteins: conformational sampling and reconstruction of folding kinetics.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Interaction of an ionic complementary peptide with a hydrophobic graphite surface

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Conformational sampling and energetics of drug-like molecules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Self-guided Langevin dynamics study of regulatory interactions in NtrC.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Open science grid study of the coupling between conformation and water content in the interior of a protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Computational techniques for efficient conformational sampling of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Analyzing the performance of conformational search programs on compound databases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Molecular dynamics: survey of methods for simulating the activity of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Characterizing the nature of virtual amorphous silicon

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Advances in biomolecular simulations: methodology and recent applications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Conformational sampling for the impatient

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Exploring the conformational space of membrane protein folds matching distance constraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

An evolutionary approach for structure-based design of natural and non-natural peptidic ligands

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Functional preference of the constituent amino acid residues in a phage-library-based nonphosphorylated inhibitor of the Grb2-SH2 domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Calculation of protein conformation by global optimization of a potential energy function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

The fundamentals of protein folding: bringing together theory and experiment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

QXP: powerful, rapid computer algorithms for structure-based drug design.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

A genetic algorithm based molecular modeling technique for RNA stem-loop structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Folding of immunogenic peptide fragments of proteins in water solution. II. The nascent helix

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Potential of genetic algorithms in protein folding and protein engineering simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3731171

Conformational analysis using distance geometry methods.

3 June 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: comparison with distance geometry calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Exhaustive conformational search and simulated annealing for models of lattice peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

A deterministic algorithm for constrained enumeration of transmembrane protein folds.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Simulation of peptide folding with explicit water--a mean solvation method.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Application of accelerated molecular dynamics schemes to the production of amorphous silicon.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Directionally negative friction: a method for enhanced sampling of rare event kinetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F9781118197714.CH6

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Nanosecond time scale folding dynamics of a pentapeptide in water

1 reference

12 December 2020

Targeted molecular dynamics: a new approach for searching pathways of conformational transitions

1 reference

12 December 2020

Characterizing the denatured state of human prion 121-230

1 reference

12 December 2020

A statistical analysis of the precision of reweighting-based simulations

1 reference

12 December 2020

Enhancing QM/MM molecular dynamics sampling in explicit environments via an orthogonal-space-random-walk-based strategy

1 reference

12 December 2020

Isotropic periodic sum: a method for the calculation of long-range interactions.

1 reference

12 December 2020