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Multi‐state modeling of G‐protein coupled receptors at experimental accuracy

Proteins, structure, function, and bioinformatics, 2022-11, Vol.90 (11), p.1873-1885

2022

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ColabFold: making protein folding accessible to all

Nature methods, 2022-06, Vol.19 (6), p.679-682

2022

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Direct generation of protein conformational ensembles via machine learning

Nature communications, 2023-02, Vol.14 (1), p.774-14, Article 774

2023

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GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

Nucleic acids research, 2017-07, Vol.45 (W1), p.W320-W324

2017

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GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

Scientific reports, 2016-08, Vol.6 (1), p.32153-32153, Article 32153

2016

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Driven to near‐experimental accuracy by refinement via molecular dynamics simulations

Proteins, structure, function, and bioinformatics, 2019-12, Vol.87 (12), p.1263-1275

2019

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The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

Proteins, structure, function, and bioinformatics, 2018-03, Vol.86 (S1), p.257-273

2018

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Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB

eLife, 2022-04, Vol.11

2022

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Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments

PloS one, 2014-11, Vol.9 (11), p.e113811-e113811

2014

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Experimental accuracy in protein structure refinement via molecular dynamics simulations

Proceedings of the National Academy of Sciences - PNAS, 2018-12, Vol.115 (52), p.13276-13281

2018

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High‐accuracy protein structures by combining machine‐learning with physics‐based refinement

Proteins, structure, function, and bioinformatics, 2020-05, Vol.88 (5), p.637-642

2020

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One bead per residue can describe all-atom protein structures

Structure (London), 2024-01, Vol.32 (1), p.97-111.e6

2024

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GalaxyRefine: Protein structure refinement driven by side-chain repacking

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W384-W388

2013

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What makes it difficult to refine protein models further via molecular dynamics simulations?

Proteins, structure, function, and bioinformatics, 2018-03, Vol.86 (S1), p.177-188

2018

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PREFMD: a web server for protein structure refinement via molecular dynamics simulations

Bioinformatics, 2018-03, Vol.34 (6), p.1063-1065

2018

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GalaxyWEB server for protein structure prediction and refinement

Nucleic acids research, 2012-07, Vol.40 (Web Server issue), p.W294

2012

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GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization

Nucleic acids research, 2015-07, Vol.43 (W1), p.W431-W435

2015

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Effective protein model structure refinement by loop modeling and overall relaxation

Proteins, structure, function, and bioinformatics, 2016-09, Vol.84 (S1), p.293-301

2016

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Protein assembly and crowding simulations

Current opinion in structural biology, 2022-04, Vol.73, p.102340-102340, Article 102340

2022

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GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

Nucleic acids research, 2019-07, Vol.47 (W1), p.W451-W455

2019

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Physics‐based protein structure refinement in the era of artificial intelligence

Proteins, structure, function, and bioinformatics, 2021-12, Vol.89 (12), p.1870-1887

2021

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Protein Structure Refinement via Molecular Dynamics Simulations

Biophysical journal, 2018-02, Vol.114 (3), p.575a-575a

2018

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GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential

Journal of chemical information and modeling, 2021-05, Vol.61 (5), p.2283-2293

2021

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GalaxyWEB server for protein structure prediction and refinement

Nucleic acids research, 2012-07, Vol.40 (W1), p.W294-W297

2012

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Structure refinement of membrane proteins via molecular dynamics simulations

Proteins, structure, function, and bioinformatics, 2018-07, Vol.86 (7), p.738-750

2018

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Multi‐state modeling of G‐protein coupled receptors at experimental accuracy

ColabFold: making protein folding accessible to all

Direct generation of protein conformational ensembles via machine learning

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

Driven to near‐experimental accuracy by refinement via molecular dynamics simulations

The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments

Experimental accuracy in protein structure refinement via molecular dynamics simulations

High‐accuracy protein structures by combining machine‐learning with physics‐based refinement

One bead per residue can describe all-atom protein structures

GalaxyRefine: Protein structure refinement driven by side-chain repacking

What makes it difficult to refine protein models further via molecular dynamics simulations?

PREFMD: a web server for protein structure refinement via molecular dynamics simulations

GalaxyWEB server for protein structure prediction and refinement

GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization

Effective protein model structure refinement by loop modeling and overall relaxation

Protein assembly and crowding simulations

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

Physics‐based protein structure refinement in the era of artificial intelligence

Protein Structure Refinement via Molecular Dynamics Simulations

GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential

GalaxyWEB server for protein structure prediction and refinement

Structure refinement of membrane proteins via molecular dynamics simulations

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