(Q38270534)

English

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

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

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

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

2

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author name string

Hongyi Zhou

1

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

publication date

1 November 2002

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Protein Science

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

11

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

11

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

2714-2726

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Statistical potentials for fold assessment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

1 reference

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6 September 2017

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

1 reference

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6 September 2017

Ab initio construction of protein tertiary structures using a hierarchical approach

1 reference

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6 September 2017

Effective energy functions for protein structure prediction.

1 reference

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6 September 2017

The introduction of strain and its effects on the structure and stability of T4 lysozyme

1 reference

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6 September 2017

Knowledge-based interaction potentials for proteins.

1 reference

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6 September 2017

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

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6 September 2017

Designing potential energy functions for protein folding

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6 September 2017

Effective energy function for proteins in solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

1 reference

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6 September 2017

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

1 reference

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6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Protein folding simulations with genetic algorithms and a detailed molecular description

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Energy functions that discriminate X-ray and near native folds from well-constructed decoys

1 reference

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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

1 reference

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An empirical energy function for threading protein sequence through the folding motif

1 reference

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6 September 2017

Reduced representation model of protein structure prediction: statistical potential and genetic algorithms

1 reference

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6 September 2017

Recognition of errors in three-dimensional structures of proteins

1 reference

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Comparison of systematic search and database methods for constructing segments of protein structure

1 reference

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Ranking potential binding peptides to MHC molecules by a computational threading approach

1 reference

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6 September 2017

A new approach to protein fold recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Assessment of protein models with three-dimensional profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

6 September 2017

Fast and simple Monte Carlo algorithm for side chain optimization in proteins: application to model building by homology

1 reference

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Selection of representative protein data sets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

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Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

1 reference

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Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A.

1 reference

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Comparison of database potentials and molecular mechanics force fields

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An algorithm for determining the conformation of polypeptide segments in proteins by systematic search

1 reference

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23 June 2018

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

23 June 2018

Identifying native-like protein structures using physics-based potentials

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

31 August 2018

Comparison of two optimization methods to derive energy parameters for protein folding: perceptron and Z score.

1 reference

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31 August 2018

MONSSTER: a method for folding globular proteins with a small number of distance restraints

1 reference

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31 August 2018

Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2373736

31 August 2018

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1 reference

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1 reference

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1 reference

https://api.crossref.org/works/10.1110%2FPS.0217002

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https://api.crossref.org/works/10.1110%2FPS.0217002

21 January 2018

The GROMOS Biomolecular Simulation Program Package

1 reference

https://api.crossref.org/works/10.1110%2FPS.0217002

21 January 2018

Knowledge-based validation of protein structure coordinates derived by X-ray crystallography and NMR spectroscopy

1 reference

https://api.crossref.org/works/10.1110%2FPS.0217002

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1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

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based on heuristic

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Derivation of protein-specific pair potentials based on weak sequence fragment similarity

1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

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based on heuristic

inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force

1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A critical assessment of comparative molecular modeling of tertiary structures of proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

1 reference

https://pubmed.ncbi.nlm.nih.gov/12381853

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1110/PS.0217002

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

1 September 2017

ResearchGate publication ID

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