(Q30376344)

English

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation

scientific article

In more languages

Statements

scholarly article

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation (English)

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

protein structure

0 references

Harold A. Scheraga

4

object named as

Harold A Scheraga

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

author name string

Yelena A Arnautova

1

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

Yury N Vorobjev

2

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

Jorge A Vila

3

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

language of work or name

0 references

publication date

1 October 2009

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

77

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

1

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

38-51

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Use of decoys to optimize an all-atom force field including hydration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Protein structure prediction by all-atom free-energy refinement.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Near-native structure refinement using in vacuo energy minimization.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Protein structure evaluation using an all-atom energy based empirical scoring function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Comparison between Generalized-Born and Poisson-Boltzmann methods in physics-based scoring functions 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=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

An all-atom force field for tertiary structure prediction of helical proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent 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=4502597

20 June 2018

Automated structure prediction of weakly homologous proteins on a genomic scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

An improved protein decoy set for testing energy functions 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=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Free energies of protein decoys provide insight into determinants of protein stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 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=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Theoretical and experimental studies of conformations of polypeptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Principles that govern the folding of protein chains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Monte Carlo-minimization approach to the multiple-minima problem in protein folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method--tests on poly(L-alanine).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

20 June 2018

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

26 November 2018

MOPED: method for optimizing physical energy parameters using decoys.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

26 November 2018

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Born solvent model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4502597

26 November 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=4502597

26 November 2018

Application of statistical potentials to protein structure refinement from low resolution ab initio models

1 reference

https://pubmed.ncbi.nlm.nih.gov/19384995

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/19384995

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/19384995

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1002/PROT.22414

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

release_ybppbza7hfdr3hvzqilq3asaky

1 reference

https://api.fatcat.wiki/v0/release/ybppbza7hfdr3hvzqilq3asaky

24 November 2022

based on heuristic

mapped directly with Wikidata item

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

10 August 2017

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q30376344&oldid=1838391207"