Lim Heo

发表

Structure refinement of membrane proteins via molecular dynamics simulations

Michael Feig, Lim Heo, Bercem Dutagaci, 2018, Proteins.

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

M. Feig, Lim Heo, G. Janson, 2021, Proteins.

Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

Chaok Seok, Gyu Rie Lee, Hahnbeom Park, 2014, PloS one.

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

Collin F Arbour, M. Feig, Lim Heo, 2021, Journal of chemical theory and computation.

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

Gyu Rie Lee, Chaok Seok, Lim Heo, 2019, Nucleic Acids Res..

New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X‐ray crystallography and docking studies

Chaok Seok, D. Shin, Mi‐Sun Kim, 2013, Proteins.

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

Chaok Seok, Lim Heo, J. Choe, 2014, Protein science : a publication of the Protein Society.

Direct generation of protein conformational ensembles via machine learning

M. Feig, Lim Heo, G. Janson, 2022, bioRxiv.

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

Collin F Arbour, M. Feig, Lim Heo, 2020, Journal of chemical theory and computation.

Modeling concentration-dependent phase separation processes involving peptides and RNA via residue-based coarse-graining

M. Feig, L. Lapidus, Lim Heo, 2022, bioRxiv.

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

M. Feig, E. Hegg, Lim Heo, 2021, Critical reviews in biochemistry and molecular biology.

GalaxyRefine: protein structure refinement driven by side-chain repacking

Chaok Seok, Hahnbeom Park, Lim Heo, 2013, Nucleic Acids Res..

GalaxyWEB server for protein structure prediction and refinement

Chaok Seok, Hahnbeom Park, Lim Heo, 2012, Nucleic Acids Res..

LigDockCSA: Protein–ligand docking using conformational space annealing

Jooyoung Lee, Chaok Seok, Juyong Lee, 2011, J. Comput. Chem..

Experimental accuracy in protein structure refinement via molecular dynamics simulations

Michael Feig, Lim Heo, M. Feig, 2018, Proceedings of the National Academy of Sciences.

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

Chaok Seok, Lim Heo, J. Roe, 2013, Proteins.

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

M. Feig, Lim Heo, L. Kroos, 2021, bioRxiv.

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

M. Feig, Lim Heo, 2021, bioRxiv.

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

Daisuke Kihara, Keehyoung Joo, Daisuke Kuroda, 2016, Proteins.

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

Minkyung Baek, Chaok Seok, Taeyong Park, 2017, Nucleic Acids Res..

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

Chaok Seok, Hasup Lee, Lim Heo, 2016, Scientific Reports.

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

Hasup Lee, Chaok Seok, Lim Heo, 2015, Nucleic Acids Res..

Protein assembly and crowding simulations.

Y. Sugita, M. Feig, Lim Heo, 2022, Current opinion in structural biology.

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

Michael Feig, Lim Heo, M. Feig, 2020, bioRxiv.

Effective protein model structure refinement by loop modeling and overall relaxation

Chaok Seok, Gyu Rie Lee, Lim Heo, 2016, Proteins.

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

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

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

Chaok Seok, Lim Heo, Hasup Lee, 2016, Methods in molecular biology.

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

Chaok Seok, Woong-Hee Shin, Lim Heo, 2014, Nucleic Acids Res..

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

Chaok Seok, Gyu Rie Lee, Lim Heo, 2018, Proteins.

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

Michael Feig, Lim Heo, M. Feig, 2020, Proteins.

High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement

Michael Feig, Lim Heo, M. Feig, 2019, bioRxiv.

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server.

Minkyung Baek, Chaok Seok, Taeyong Park, 2020, Methods in molecular biology.

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

Ashutosh Kumar Singh, Chaok Seok, Lim Heo, 2015, Molecular microbiology.

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

Michael Feig, Lim Heo, M. Feig, 2018, Proteins.

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

Sameer Velankar, Minkyung Baek, Chaok Seok, 2018, Proteins.

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

M. Feig, L. Lapidus, Lim Heo, 2022, bioRxiv.

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

Michael Feig, Lim Heo, M. Feig, 2018, Bioinform..

One particle per residue is sufficient to describe all-atom protein structures

M. Feig, Lim Heo, 2023, bioRxiv.

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

Michael Feig, Lim Heo, Collin F Arbour, 2019, Proteins.

One bead per residue can describe all-atom protein structures.

M. Feig, Lim Heo, 2023, Structure.

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

Chaok Seok, Lim Heo, Sangwoo Park, 2021, J. Chem. Inf. Model..

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

Chaok Seok, Lim Heo, J. Roe, 2013, Proteins.