(Q25256785)

6 July 2017

title

A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators (English)

1 reference

6 July 2017

Federico Fogolari

1

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Giorgio Colombo

object named as

Giorgio Colombo

series ordinal

3

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author name string

Silvio C E Tosatto

series ordinal

2

1 reference

6 July 2017

language of work or name

English

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publication date

14 December 2005

1 reference

6 July 2017

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6 July 2017

volume

6

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6 July 2017

issue

1

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page(s)

301

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Improved protein structure selection using decoy-dependent discriminatory functions

6 July 2017

cites work

1 reference

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Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

7 April 2017

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

7 April 2017

1 reference

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Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

7 April 2017

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The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

7 April 2017

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Discrimination of the native from misfolded protein models with an energy function including implicit solvation

7 April 2017

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

7 April 2017

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GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences

7 April 2017

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7 April 2017

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The victor/FRST function for model quality estimation.

7 April 2017

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High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

28 September 2017

1 reference

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28 September 2017

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

28 September 2017

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Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

28 September 2017

1 reference

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

28 September 2017

1 reference

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Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

28 September 2017

1 reference

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2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15.

28 September 2017

1 reference

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A distance-dependent atomic knowledge-based potential for improved protein structure selection.

28 September 2017

1 reference

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Free energy determinants of tertiary structure and the evaluation of protein models.

28 September 2017

1 reference

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Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Biomolecular electrostatics with the linearized Poisson-Boltzmann equation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Composites of local structure propensities: evidence for local encoding of long-range structure

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

Molecular mechanics and dynamics of biomolecules using a solvent continuum model.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1351271

A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

28 November 2018

1 reference

12 December 2020

Protein refinement: a new challenge for CASP in its 10th anniversary

1 reference

12 December 2020

Molecular mechanisms for cooperative folding of proteins

1 reference

12 December 2020

MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: Free energy gradients in conformational transitions?

1 reference

12 December 2020

Free-Energy Landscape of the Villin Headpiece in an All-Atom Force Field

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2105-6-301

1 reference

journals/bmcbi/FogolariTC05

6 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

6 July 2017

1 reference