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 (Q57134711)

From Wikidata

Jump to navigation Jump to search

article

Language	Label	Description	Also known as
English	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	article

Statements

scholarly article

0 references

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 (English)

0 references

0 references

Emilio Gallicchio

object named as

Emilio Gallicchio

2

0 references

Anders Wallqvist

object named as

Anders Wallqvist

3

0 references

author name string

Anthony K Felts

1

0 references

Ronald M Levy

4

0 references

language of work or name

0 references

publication date

1 August 2002

0 references

0 references

48

0 references

2

0 references

404-22

0 references

Effective energy functions for protein structure prediction.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Potential energy functions for threading

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Simplified proteins: minimalist solutions to the 'protein folding problem'.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Designing potential energy functions for protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Ab initio protein folding.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Free energy determinants of tertiary structure and the evaluation of protein models.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Identifying native-like protein structures using physics-based potentials

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Generalized born models of macromolecular solvation effects

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Solvation energy in protein folding and binding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Evaluation of protein models by atomic solvation preference.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Molecular mechanics in biology: from structure to function, taking account of solvation

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Electrostatic contributions to molecular free energies in solution

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Electrostatic interactions in macromolecules: theory and applications

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Electrostatic Energy and Macromolecular Function

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Semianalytical treatment of solvation for molecular mechanics and dynamics

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Implicit solvent models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Knowledge-based potentials for proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Structure-derived potentials and protein simulations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Identification of cooperative folding units in a set of native proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Conformations of folded proteins in restricted spaces

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

An analysis of incorrectly folded protein models. Implications for structure predictions.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Protein model structure evaluation using the solvation free energy of folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Discriminating compact nonnative structures from the native structure of globular proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

A new computational model for protein folding based on atomic solvation

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Disulphide bridges in globular proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Accurate modeling of protein conformation by automatic segment matching

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

A lattice model for protein structure prediction at low resolution

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Sequence-specific proton NMR assignments and solution structure of bovine pancreatic polypeptide

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

The repeating segments of the F-actin cross-linking gelation factor (ABP-120) have an immunoglobulin-like fold

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Dominant forces in protein folding

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Evaluation of the conformational free energies of loops in proteins.

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Effective energy function for proteins in solution

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Criteria that discriminate between native proteins and incorrectly folded models

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Factors affecting the ability of energy functions to discriminate correct from incorrect folds

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Protein fold recognition and dynamics in the space of contact maps

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

A critical assessment of comparative molecular modeling of tertiary structures of proteins

1 reference

https://api.crossref.org/works/10.1002%2FPROT.10171

21 January 2018

Identifiers

10.1002/PROT.10171

0 references

0 references

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=Q57134711&oldid=1527088467"