(Q41833277)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

author name string

Song Liu

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

Hongyi Zhou

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

Yaoqi Zhou

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

publication date

1 February 2004

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

page(s)

400-411

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

Simplicial edge representation of protein structures and alpha contact potential with confidence measure.

17 November 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

An improved protein decoy set for testing energy functions for protein structure prediction.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

TOUCHSTONE II: a new approach to ab initio protein structure prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Genome-wide studies of protein-protein interaction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Protein-protein docking predictions for the CAPRI experiment

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Discrimination of native protein structures using atom-atom contact scoring

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Development of unified statistical potentials describing protein-protein interactions.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Packing helices in proteins by global optimization of a potential energy function

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Analysing six types of protein-protein interfaces

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Evaluating CASP4 predictions with physical energy functions.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A protein folding potential that places the native states of a large number of proteins near a local minimum

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Protein structure prediction in 2002.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Statistical potentials for fold assessment.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Protein structure prediction and structural genomics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Identification of protein oligomerization states by analysis of interface conservation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Prospects for ab initio protein structural genomics.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Ab initio construction of protein tertiary structures using a hierarchical approach

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Effective energy functions for protein structure prediction.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Environment-dependent residue contact energies for proteins.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Protein folding: from the levinthal paradox to structure prediction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Ab initio protein structure prediction of CASP III targets using ROSETTA

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A combined approach for ab initio construction of low resolution protein tertiary structures from sequence.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

VERIFY3D: assessment of protein models with three-dimensional profiles

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

From Levinthal to pathways to funnels

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Verification of protein structures: patterns of nonbonded atomic interactions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Recognition of errors in three-dimensional structures of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A new approach to protein fold recognition

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A lattice model for protein structure prediction at low resolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Selection of representative protein data sets

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A simplified representation of protein conformations for rapid simulation of protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Quantifying the effect of burial of amino acid residues on protein stability.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Residue frequencies and pairing preferences at protein-protein interfaces.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Discriminating between homodimeric and monomeric proteins in the crystalline state.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Combination of threading potentials and sequence profiles improves fold recognition.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Use of pair potentials across protein interfaces in screening predicted docked complexes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Statistical potentials extracted from protein structures: how accurate are they?

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286718

An empirical energy potential with a reference state for protein fold and sequence recognition

18 August 2018

1 reference

12 December 2020

Distance-dependent, pair potential for protein folding: results from linear optimization

1 reference

12 December 2020

Modeling of protein interactions in genomes

1 reference

12 December 2020

De Novo Prediction of Three-dimensional Structures for Major Protein Families

1 reference

12 December 2020

Atomic contact vectors in protein‐protein recognition

1 reference

12 December 2020

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

12 December 2020

Protein Folding: A Perspective from Theory and Experiment.

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.03348304

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739325%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1 reference