(Q30415550)

21 June 2017

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations (English)

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molecular dynamics simulation

21 June 2017

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4

Ron O Dror

1 reference

21 June 2017

Alpan Raval

1

1 reference

21 June 2017

Stefano Piana

series ordinal

2

1 reference

21 June 2017

Michael P Eastwood

series ordinal

3

1 reference

21 June 2017

David E Shaw

series ordinal

5

1 reference

21 June 2017

language of work or name

English

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publication date

15 May 2012

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21 June 2017

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21 June 2017

80

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21 June 2017

2071-2079

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21 June 2017

8

1 reference

ProFunc: a server for predicting protein function from 3D structure

21 June 2017

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Protein structure prediction: when is it useful?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

I-TASSER: a unified platform for automated protein structure and function prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

An integrated in silico 3D model-driven discovery of a novel, potent, and selective amidosulfonamide 5-HT1A agonist (PRX-00023) for the treatment of anxiety and depression

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

In silico pharmacology for drug discovery: applications to targets and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Old friends in new guise: repositioning of known drugs with structural bioinformatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Evaluating the usefulness of protein structure models for molecular replacement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

High-resolution structure prediction and the crystallographic phase problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Assessment of the protein-structure refinement category in CASP8

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Assessment of protein structure refinement in CASP9.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Progress over the first decade of CASP experiments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Reliable protein structure refinement using a physical energy function

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Near-native structure refinement using in vacuo energy minimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Refining homology models by combining replica-exchange molecular dynamics and statistical potentials

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

An efficient conformational sampling method for homology modeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Sampling bottlenecks in de novo protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Molecular dynamics in the endgame of protein structure prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Solvent dramatically affects protein structure refinement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Recent advances in implicit solvent-based methods for biomolecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

How fast-folding proteins fold

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Systematic validation of protein force fields against experimental data

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

How robust are protein folding simulations with respect to force field parameterization?

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Atomic-level characterization of the structural dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

VMD: visual molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Reversible multiple time scale molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Canonical dynamics: Equilibrium phase-space distributions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24098

21 January 2018

Identifiers

DOI

10.1002/PROT.24098

1 reference

21 June 2017

1 reference