Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field (Q36881617)

16 August 2017

Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field (English)

1 reference

16 August 2017

0 references

0 references

3

Harold A Scheraga

1 reference

16 August 2017

2

Cezary Czaplewski

1 reference

16 August 2017

Marian Nanias

1

1 reference

16 August 2017

1 January 2006

1 reference

Journal of Chemical Theory and Computation

16 August 2017

1 reference

16 August 2017

2

1 reference

16 August 2017

3

1 reference

16 August 2017

513-528

1 reference

16 August 2017

The Monte Carlo method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

The free energy landscape for beta hairpin folding in explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Structural analysis of WW domains and design of a WW prototype

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Solution structure of the albumin-binding GA module: a versatile bacterial protein domain

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

New Monte Carlo algorithm: Entropic sampling.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Low-energy structures of two dipeptides and their relationship to bend conformations.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine).

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

The multiple-minima problem in the conformational analysis of polypeptides. III. An electrostatically driven Monte Carlo method: tests on enkephalin.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Efficient sampling of protein structures by model hopping.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Replica-exchange extensions of simulated tempering method

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Replica-exchange method using the generalized effective potential

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Parallel tempering simulations of HP-36.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

Replica Monte Carlo simulation of spin glasses.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2538381

A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18797518

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Optimized Monte Carlo data analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18797518

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18797518

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT050253O

1 reference

16 August 2017

1 reference

PMC publication ID

2538381

16 August 2017

PubMed publication ID

18797518

1 reference

PMC publication ID

2538381