List of works - Lim Heo

Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

scientific article published on 17 June 2013

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

scientific article

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.

scientific article

ColabFold: making protein folding accessible to all

scientific article published on 30 May 2022

Direct generation of protein conformational ensembles via machine learning

scientific article published in 2023

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

scientific article published on 24 June 2019

Effective protein model structure refinement by loop modeling and overall relaxation

scientific article

Experimental accuracy in protein structure refinement via molecular dynamics simulations

scientific article published on 10 December 2018

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds

scientific article

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

scientific article

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

scientific article published on 12 May 2015

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

scientific article published on 01 July 2019

GalaxyRefine: Protein structure refinement driven by side-chain repacking

scientific article

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

scientific article published on 18 August 2016

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

scientific article

GalaxyWEB server for protein structure prediction and refinement

scientific article

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

scientific article published on 15 November 2019

LigDockCSA: protein-ligand docking using conformational space annealing.

scientific article published on 12 August 2011

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

scientific article published on 01 January 2020

Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement

scientific article (preprint)

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

scientific article published in 2022

New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

scientific article

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

scientific article published on 8 November 2017

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

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

scientific article

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

scientific article published on 16 October 2017

Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif

scientific article

Structure refinement of membrane proteins via molecular dynamics simulations

scientific article published on 06 May 2018

The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.

scientific article published on 10 November 2017

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

scientific article published on 4 October 2017

List of works by Lim Heo

Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.

ColabFold: making protein folding accessible to all

Direct generation of protein conformational ensembles via machine learning

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

Effective protein model structure refinement by loop modeling and overall relaxation

Experimental accuracy in protein structure refinement via molecular dynamics simulations

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds

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

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

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

GalaxyRefine: Protein structure refinement driven by side-chain repacking

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

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

GalaxyWEB server for protein structure prediction and refinement

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

LigDockCSA: protein-ligand docking using conformational space annealing.

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement

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

New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

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

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

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

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif

Structure refinement of membrane proteins via molecular dynamics simulations

The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.

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