(Q33813152)

29 July 2017

title

Methods for Monte Carlo simulations of biomacromolecules (English)

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29 July 2017

1 reference

Andreas Vitalis

1

1 reference

29 July 2017

Rohit V Pappu

series ordinal

2

1 reference

29 July 2017

publication date

1 January 2009

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Annual reports in computational chemistry

29 July 2017

published in

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29 July 2017

volume

5

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29 July 2017

page(s)

49-76

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

29 July 2017

cites work

1 reference

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Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength.

4 July 2018

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Collapse transition in proteins

4 July 2018

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Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment

4 July 2018

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Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization

4 July 2018

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Protein structure prediction using basin-hopping.

4 July 2018

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ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Recent advances in implicit solvent-based methods for biomolecular simulations

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations.

4 July 2018

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Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane.

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo

4 July 2018

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Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Quaternions in molecular modeling

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Biomolecular modeling: Goals, problems, perspectives

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Classical statistical mechanics of constraints: a theorem and application to polymers

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Scalable molecular dynamics with NAMD

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Improving implicit solvent simulations: a Poisson-centric view

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

The flexibility in the proline ring couples to the protein backbone

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Monte Carlo studies of folding, dynamics, and stability in alpha-helices

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Understanding protein folding with energy landscape theory. Part II: Quantitative aspects

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Understanding protein folding with energy landscape theory. Part I: Basic concepts

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Rotamer libraries in the 21st century

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Preferred proline puckerings in cis and trans peptide groups: implications for collagen stability

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Collective Monte Carlo Updating for Spin Systems

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Nonuniversal critical dynamics in Monte Carlo simulations

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Exploring the energy landscape in proteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Dynamics of folded proteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Multiscale Monte Carlo algorithm for simple fluids.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Min-map bias Monte Carlo for chain molecules: biased Monte Carlo sampling based on bijective minimum-to-minimum mapping.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

PROFASI: A Monte Carlo simulation package for protein folding and aggregation.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Adaptive time stepping in biomolecular dynamics

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Monte Carlo simulations of biomolecules: The MC module in CHARMM.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Generalized geometric cluster algorithm for fluid simulation.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Combining smart darting with parallel tempering using Eckart space: application to Lennard-Jones clusters.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Density guided importance sampling: application to a reduced model of protein folding.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Rejection-free geometric cluster algorithm for complex fluids.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

A kinematic view of loop closure

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

On the kinematics of protein folding.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Cool walking: a new Markov chain Monte Carlo sampling method

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Distance and exposure dependent effective dielectric function

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

Convergence of sampling in protein simulations.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2860296

A complete conformational map for RNA

30 October 2018

1 reference

12 December 2020

The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation

1 reference

12 December 2020

Slow relaxation and solvent effects in the collapse of a polymer

1 reference

12 December 2020

Generalization of the Wang-Landau method for off-lattice simulations

1 reference

12 December 2020

Multiple "time step" Monte Carlo simulations: application to charged systems with Ewald summation

1 reference

12 December 2020

All-atom Monte Carlo simulation of GCAA RNA folding

1 reference

12 December 2020

Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians

1 reference

12 December 2020

Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors

1 reference

12 December 2020

A simple method of estimating sampling consistency based on free energy map distance

1 reference

12 December 2020

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

1 reference

12 December 2020

Efficient Generalized Born Models for Monte Carlo Simulations.

1 reference

12 December 2020

Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model

1 reference

12 December 2020

Monte Carlo vs Molecular Dynamics for Conformational Sampling

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Equation of State Calculations by Fast Computing Machines

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Die Berechnung optischer und elektrostatischer Gitterpotentiale

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Self-assembly of sparsely distributed molecules: An efficient cluster algorithm

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Molecular dynamics with coupling to an external bath

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https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Configurational bias Monte Carlo: a new sampling scheme for flexible chains

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https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Novel scheme to study structural and thermal properties of continuously deformable molecules

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https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Improving the efficiency of the configurational-bias Monte Carlo algorithm

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

Recoil growth algorithm for chain molecules with continuous interactions

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

A smooth particle mesh Ewald method

1 reference

https://api.crossref.org/works/10.1016%2FS1574-1400%2809%2900503-9

7 January 2021

10.1016/S1574-1400(09)00503-9

Identifiers

DOI

1 reference

29 July 2017

1 reference

29 July 2017

1 reference