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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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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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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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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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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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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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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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GalaxySite: ligand-binding-site prediction by using molecular docking

Nucleic acids research, 2014-07, Vol.42 (Web Server issue), p.W210-W214

2014

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Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation

Journal of chemical theory and computation, 2021-03, Vol.17 (3), p.1931-1943

2021

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Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

Methods in molecular biology (Clifton, N.J.), 2020-01, Vol.2165, p.127

2020

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Characterizing Transient Protein–Protein Interactions by Trp-Cys Quenching and Computer Simulations

The journal of physical chemistry letters, 2022-11, Vol.13 (43), p.10175-10182

2022

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Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer

Critical reviews in biochemistry and molecular biology, 2021-11, Vol.56 (6), p.640-668

2021

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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

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

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

Effective protein model structure refinement by loop modeling and overall relaxation

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

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

Structure refinement of membrane proteins via molecular dynamics simulations

GalaxySite: ligand-binding-site prediction by using molecular docking

Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

Characterizing Transient Protein–Protein Interactions by Trp-Cys Quenching and Computer Simulations

Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer

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