(Q36870684)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

title

Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

2

1 reference

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14 January 2020

author name string

Anthony K Felts

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Dmitriy Chekmarev

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Kristina A Paris

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Richard A Friesner

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

Ronald M Levy

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

language of work or name

1 reference

1 January 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

14 January 2020

published in

1 reference

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14 January 2020

volume

4

1 reference

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14 January 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

page(s)

855-868

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

Generalized Born model with a simple, robust molecular volume correction

14 January 2020

cites work

1 reference

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A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing.

29 September 2017

1 reference

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Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

29 September 2017

1 reference

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In quest of an empirical potential for protein structure prediction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Comparative modeling for protein structure prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Novel procedure for modeling ligand/receptor induced fit effects.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Progress over the first decade of CASP experiments.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Improved protein structure selection using decoy-dependent discriminatory functions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

A hierarchical approach to all-atom protein loop prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

An improved protein decoy set for testing energy functions for protein structure prediction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

PISCES: a protein sequence culling server

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Multiplexed-replica exchange molecular dynamics method for protein folding simulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Evaluating CASP4 predictions with physical energy functions.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

The free energy landscape for beta hairpin folding in explicit water

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Modeling of loops in protein structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Effective energy functions for protein structure prediction.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Ab initio protein structure prediction of CASP III targets using ROSETTA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Long loop prediction using the protein local optimization program.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Atomically detailed potentials to recognize native and approximate protein structures.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Refinement of NMR structures using implicit solvent and advanced sampling techniques

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute-solvent van der Waals interactions

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Atomic simulations of protein folding, using the replica exchange algorithm.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Identifying native-like protein structures using physics-based potentials

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Replica-Exchange Monte Carlo Scheme for Bayesian Data Analysis

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2533438

Exploring the energy landscape of a beta hairpin in explicit solvent

4 December 2018

1 reference

12 December 2020

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

12 December 2020

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

1 reference

12 December 2020

Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain

1 reference

12 December 2020

Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling

1 reference

12 December 2020

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

1 reference

12 December 2020

All-exchanges parallel tempering

1 reference

12 December 2020

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

1 reference

12 December 2020

Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects.

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT800051K

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18787648%20AND%20SRC:MED&resulttype=core&format=json

14 January 2020

1 reference