(Q34309528)

1 August 2017

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title

Generalized-ensemble algorithms for molecular simulations of biopolymers (English)

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1 August 2017

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Mitsutake A

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1 August 2017

Sugita Y

series ordinal

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1 August 2017

Okamoto Y

series ordinal

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1 August 2017

publication date

1 January 2001

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1 August 2017

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1 August 2017

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1 August 2017

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1 August 2017

page(s)

96-123

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

1 August 2017

cites work

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Multicanonical ensemble: A new approach to simulate first-order phase transitions

21 January 2018

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21 January 2018

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Adaptive umbrella sampling: Self-consistent determination of the non-Boltzmann bias

21 January 2018

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Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

21 January 2018

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New Monte Carlo algorithms for protein folding.

21 January 2018

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Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide

21 January 2018

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On the origin of the cooperativity of protein folding: implications from model simulations

21 January 2018

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Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics simulation.

21 January 2018

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Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

21 January 2018

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Temperature dependence of distributions of conformations of a small peptide.

21 January 2018

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Monte Carlo simulations in generalized ensemble: Multicanonical algorithm versus simulated tempering.

21 January 2018

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Possible generalization of Boltzmann-Gibbs statistics

21 January 2018

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Characteristic temperatures of folding of a small peptide

21 January 2018

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The folding funnel landscape for the peptide Met-enkephalin

21 January 2018

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Optimization by Simulated Annealing

21 January 2018

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Generalized simulated annealing algorithms using Tsallis statistics: Application to conformational optimization of a tetrapeptide.

21 January 2018

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Novel methods of sampling phase space in the simulation of biological systems

21 January 2018

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Replica Monte Carlo simulation of spin glasses.

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

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Equation of State Calculations by Fast Computing Machines

21 January 2018

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Alpha-helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A.

21 January 2018

1 reference

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Energetic coupling between DNA bending and base pair opening

21 January 2018

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Dependence on the dielectric model and pH in a synthetic helical peptide studied by Monte Carlo simulated annealing

21 January 2018

1 reference

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Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.

21 January 2018

1 reference

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Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

The missing term in effective pair potentials

21 January 2018

1 reference

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An all atom force field for simulations of proteins and nucleic acids

21 January 2018

1 reference

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

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Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

A direct comparison of helix propensity in proteins and peptides

21 January 2018

1 reference

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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

21 January 2018

1 reference

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Raster3D Version 2.0. A program for photorealistic molecular graphics

21 January 2018

1 reference

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RASMOL: biomolecular graphics for all

21 January 2018

1 reference

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Monte Carlo-minimization approach to the multiple-minima problem in protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Replica-exchange molecular dynamics simulation for supercooled liquids

21 January 2018

1 reference

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Comment on "Monte Carlo Simulation of a First-Order Transition for Protein Folding"

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

α-Helix Propensities of Amino Acids Studied by Multicanonical Algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Effects of Side-Chain Charges on α-Helix Stability in C-Peptide of Ribonuclease A Studied by Multicanonical Algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by multicanonical simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Multicanonical algorithm combined with the RISM theory for simulating peptides in aqueous solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Generalized-ensemble Monte Carlo method for systems with rough energy landscape

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Stochastic dynamics simulations in a new generalized ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Replica-exchange Monte Carlo method for the isobaric–isothermal ensemble

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Ab initio replica-exchange Monte Carlo method for cluster studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Replica-exchange simulated tempering method for simulations of frustrated systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Prediction of α-Helix Folding of Isolated C-Peptide of Ribonuclease A by Monte Carlo Simulated Annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Solvation structure and stability of peptides in aqueous solutions analyzed by the reference interaction site model theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

First-Principle Determination of Peptide Conformations in Solvents: Combination of Monte Carlo Simulated Annealing and RISM Theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

Peptide Conformations in Alcohol and Water: Analyses by the Reference Interaction Site Model Theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F1097-0282%282001%2960%3A2%3C96%3A%3AAID-BIP1007%3E3.0.CO%3B2-F

10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

21 January 2018

Identifiers

DOI

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1 August 2017

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