Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. (Q31037390)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739324%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

title

Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential (English)

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17 November 2019

0 references

3

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17 November 2019

Chi Zhang

series ordinal

1

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17 November 2019

author name string

Song Liu

series ordinal

2

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17 November 2019

publication date

1 February 2004

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17 November 2019

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17 November 2019

volume

13

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17 November 2019

issue

2

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17 November 2019

page(s)

391-399

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Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.

17 November 2019

cites work

1 reference

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21 June 2018

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Analysing six types of protein-protein interfaces

21 June 2018

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

21 June 2018

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21 June 2018

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

21 June 2018

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Extending the accuracy limits of prediction for side-chain conformations

21 June 2018

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

21 June 2018

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21 June 2018

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21 June 2018

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Modeling of loops in protein structures

21 June 2018

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Comparative protein structure modeling of genes and genomes

21 June 2018

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Effective energy function for proteins in solution

21 June 2018

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Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

21 June 2018

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Bayesian statistical analysis of protein side-chain rotamer preferences

21 June 2018

1 reference

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Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

PDB-based protein loop prediction: parameters for selection and methods for optimization.

21 June 2018

1 reference

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Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Origins of structural diversity within sequentially identical hexapeptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Model for haptoglobin heavy chain based upon structural homology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Selection of representative protein data sets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles.

25 November 2018

1 reference

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Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

25 November 2018

1 reference

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Improved protein loop prediction from sequence alone.

25 November 2018

1 reference

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Residue frequencies and pairing preferences at protein-protein interfaces.

25 November 2018

1 reference

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Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

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

25 November 2018

1 reference

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An automated classification of the structure of protein loops.

25 November 2018

1 reference

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

25 November 2018

1 reference

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Intrinsic phi, psi propensities of amino acids, derived from the coil regions of known structures.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2286705

Prediction of loop geometries using a generalized born model of solvation effects

25 November 2018

1 reference

12 December 2020

An all atom force field for simulations of proteins and nucleic acids

1 reference

12 December 2020

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure

1 reference

12 December 2020

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations

1 reference

12 December 2020

Prediction of the folding of short polypeptide segments by uniform conformational sampling

1 reference

12 December 2020

Identical pentapeptides with different backbones

1 reference

12 December 2020

Chameleon sequences in the PDB

1 reference

12 December 2020

Identifiers

DOI

10.1110/PS.03411904

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739324%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:14739324%20AND%20SRC:MED&resulttype=core&format=json

17 November 2019

1 reference