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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)

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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

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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)

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Emilio Gallicchio

object named as

Emilio Gallicchio

2

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Anders Wallqvist

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Anders Wallqvist

3

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author name string

Anthony K Felts

1

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Ronald M Levy

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language of work or name

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publication date

1 August 2002

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48

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2

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404-22

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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

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

21 January 2018

Potential energy functions for threading

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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

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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.

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

21 January 2018

Identifying native-like protein structures using physics-based potentials

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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

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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

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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

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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

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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 1Edited by F. Cohen

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

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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

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10.1002/PROT.10171

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