Protein model refinement using an optimized physics-based all-atom force field (Q30369943)

16 August 2017

Protein model refinement using an optimized physics-based all-atom force field (English)

1 reference

16 August 2017

1 reference

3

Jeffrey Skolnick

1 reference

16 August 2017

Anna Jagielska

1

1 reference

16 August 2017

Liliana Wroblewska

series ordinal

2

1 reference

16 August 2017

language of work or name

English

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publication date

11 June 2008

1 reference

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

16 August 2017

1 reference

16 August 2017

105

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16 August 2017

24

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16 August 2017

8268-8273

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Development of a physics-based force field for the scoring and refinement of protein models

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Physically realistic homology models built with ROSETTA can be more accurate than their templates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Toward high-resolution de novo structure prediction for small proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Practical lessons from 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=2448826

Progress and challenges in high-resolution refinement of protein structure models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Scoring function for automated assessment of protein structure template quality

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Automated structure prediction of weakly homologous proteins on a genomic scale

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Exploring protein native states and large-scale conformational changes with a modified generalized born model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Refinement of homology-based protein structures by molecular dynamics simulation techniques

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

TOUCHSTONE II: a new approach to ab initio 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=2448826

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Molecular dynamics in the endgame of 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=2448826

Pcons: a neural-network-based consensus predictor that improves fold recognition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Protein structure prediction and structural genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

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=2448826

Ab initio protein structure prediction of CASP III targets using ROSETTA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Contact order, transition state placement and the refolding rates of single domain proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2448826

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

3 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0800054105

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0800054105

Efficient Monte Carlo trial moves for polypeptide simulations.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0800054105

Prediction of the folding pathways and structure of the GCN4 leucine zipper

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18550813

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18550813

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

3D‐SHOTGUN: A novel, cooperative, fold‐recognition meta‐predictor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18550813

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0800054105

1 reference

16 August 2017

0 references

1 reference

16 August 2017

PubMed publication ID

18550813

1 reference