(Q34296935)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

title

Simple continuous and discrete models for simulating replica exchange simulations of protein folding (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

Emilio Gallicchio

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

author name string

Michael Andrec

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

Ronald M Levy

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

language of work or name

English

0 references

publication date

6 February 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

Journal of Physical Chemistry B

2 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

volume

112

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

issue

19

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

page(s)

6083-6093

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

2 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Simulating replica exchange simulations of protein folding with a kinetic network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Free energy landscapes for amyloidogenic tetrapeptides dimerization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Protein folding pathways from replica exchange simulations and a kinetic network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Entropic barriers, transition states, funnels, and exponential protein folding kinetics: a simple model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Negative activation enthalpies in the kinetics of protein folding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Temperature weighted histogram analysis method, replica exchange, and transition paths.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

On the efficiency of exchange in parallel tempering monte carlo simulations

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Protein folding kinetics and thermodynamics from atomistic simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Optimized parallel tempering simulations of proteins.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Validation of Markov state models using Shannon's entropy.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Convergence of replica exchange molecular dynamics.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Efficient sampling of protein structures by model hopping.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Optimal allocation of replicas in parallel tempering simulations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Rate-temperature relationships in lambda-repressor fragment lambda 6-85 folding

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

The incomplete beta function law for parallel tempering sampling of classical canonical systems.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Atomic simulations of protein folding, using the replica exchange algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Replica Monte Carlo simulation of spin glasses.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2978075

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

28 October 2018

1 reference

12 December 2020

Selection of temperature intervals for parallel-tempering simulations

1 reference

12 December 2020

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

1 reference

12 December 2020

A Second Look at Canonical Sampling of Biomolecules Using Replica Exchange Simulation [J. Chem. Theory Comput. 2, 1200-1202 (2006)]

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP076377+

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18251533%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

PubMed publication ID

18251533

1 reference