(Q30350721)

12 October 2017

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. (English)

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protein structure prediction

12 October 2017

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18

H A Scheraga

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12 October 2017

S Ołdziej

1

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12 October 2017

C Czaplewski

2

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12 October 2017

A Liwo

3

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12 October 2017

M Chinchio

4

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12 October 2017

M Nanias

5

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12 October 2017

J A Vila

6

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12 October 2017

M Khalili

7

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12 October 2017

Y A Arnautova

8

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12 October 2017

A Jagielska

9

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12 October 2017

M Makowski

10

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12 October 2017

H D Schafroth

11

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12 October 2017

R Kaźmierkiewicz

12

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12 October 2017

D R Ripoll

13

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12 October 2017

J Pillardy

14

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12 October 2017

J A Saunders

15

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12 October 2017

Y K Kang

16

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12 October 2017

K D Gibson

17

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12 October 2017

language of work or name

English

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publication date

13 May 2005

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Proceedings of the National Academy of Sciences of the United States of America

12 October 2017

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12 October 2017

102

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12 October 2017

21

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12 October 2017

7547-7552

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Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

TOUCHSTONE: a unified approach to protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Predictions without templates: New folds, secondary structure, and contacts in CASP5

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Critical assessment of methods of protein structure prediction (CASP)-round V.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Folding funnels: the key to robust protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

The PSIPRED protein structure prediction server

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

3 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Calculation of protein conformation by global optimization of a potential energy function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Ab initio protein structure prediction using a combined hierarchical approach.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Processing and analysis of CASP3 protein structure predictions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Protein structure prediction by global optimization of a potential energy function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

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.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Assigning amino acid sequences to 3-dimensional protein folds.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Principles that govern the folding of protein chains

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1140449

Addition of side chains to a known backbone with defined side-chain centroids

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0502655102

Determination of the Potentials of Mean Force for Rotation about Cα−CαVirtual Bonds in Polypeptides from the ab Initio Energy Surfaces of Terminally Blocked Glycine, Alanine, and Proline†

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0502655102

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0502655102

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

21 January 2018

1 reference

12 December 2020

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method

1 reference

12 December 2020

Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles

1 reference

12 December 2020

Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0502655102

1 reference

12 October 2017

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1 reference

12 October 2017

PubMed publication ID

15894609

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