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Lim Heo - Publications

Affiliations: 
Seoul National University, Seoul, South Korea 
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Heo L, Feig M. One bead per residue can describe all-atom protein structures. Structure (London, England : 1993). PMID 38000367 DOI: 10.1016/j.str.2023.10.013  0.389
2022 Heo L, Gamage K, Valdes-Garcia G, Lapidus LJ, Feig M. Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations. The Journal of Physical Chemistry Letters. 10175-10182. PMID 36279257 DOI: 10.1021/acs.jpclett.2c02723  0.344
2022 Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature Methods. 19: 679-682. PMID 35637307 DOI: 10.1038/s41592-022-01488-1  0.528
2022 Heo L, Feig M. Multi-State Modeling of G-protein Coupled Receptors at Experimental Accuracy. Proteins. PMID 35510704 DOI: 10.1002/prot.26382  0.436
2022 Olenic S, Heo L, Feig M, Kroos L. Inhibitory proteins block substrate access by occupying the active site cleft of intramembrane protease SpoIVFB. Elife. 11. PMID 35471152 DOI: 10.7554/eLife.74275  0.326
2021 Heo L, Janson G, Feig M. Physics-Based Protein Structure Refinement in the Era of Artificial Intelligence. Proteins. PMID 34156124 DOI: 10.1002/prot.26161  0.372
2021 Heo L, Park S, Seok C. GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. Journal of Chemical Information and Modeling. PMID 33938216 DOI: 10.1021/acs.jcim.0c01434  0.751
2021 Heo L, Arbour CF, Janson G, Feig M. Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation. Journal of Chemical Theory and Computation. PMID 33562962 DOI: 10.1021/acs.jctc.0c01238  0.552
2020 Baek M, Park T, Heo L, Seok C. Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. Methods in Molecular Biology (Clifton, N.J.). 2165: 127-137. PMID 32621222 DOI: 10.1007/978-1-0716-0708-4_7  0.832
2020 Heo L, Feig M. Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement. Biorxiv : the Preprint Server For Biology. PMID 32511334 DOI: 10.1101/2020.03.25.008904  0.513
2019 Heo L, Feig M. High-Accuracy Protein Structures by Combining Machine-Learning with Physics-Based Refinement. Proteins. PMID 31693199 DOI: 10.1002/Prot.25847  0.488
2019 Heo L, Arbour CF, Feig M. Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations. Proteins. PMID 31197841 DOI: 10.1002/Prot.25759  0.392
2019 Lee GR, Won J, Heo L, Seok C. GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure. Nucleic Acids Research. PMID 31001635 DOI: 10.1093/nar/gkz288  0.813
2018 Heo L, Feig M. Experimental accuracy in protein structure refinement via molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 30530696 DOI: 10.1073/Pnas.1811364115  0.401
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Heo L, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.801
2018 Dutagaci B, Heo L, Feig M. Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations. Proteins. PMID 29675899 DOI: 10.1002/Prot.25508  0.337
2017 Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. The challenge of modeling protein assemblies: The CASP12-CAPRI experiment. Proteins. PMID 29127686 DOI: 10.1002/Prot.25419  0.817
2017 Heo L, Feig M. PREFMD: a web server for protein structure refinement via molecular dynamics simulations. Bioinformatics (Oxford, England). PMID 29126101 DOI: 10.1093/Bioinformatics/Btx726  0.513
2017 Lee GR, Heo L, Seok C. Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment. Proteins. PMID 29044810 DOI: 10.1002/prot.25404  0.842
2017 Heo L, Feig M. What makes it difficult to refine protein models further via molecular dynamics simulations? Proteins. PMID 28975670 DOI: 10.1002/Prot.25393  0.366
2017 Baek M, Park T, Heo L, Park C, Seok C. GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. Nucleic Acids Research. PMID 28387820 DOI: 10.1093/Nar/Gkx246  0.855
2016 Heo L, Lee H, Seok C. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking. Scientific Reports. 6: 32153. PMID 27535582 DOI: 10.1038/srep32153  0.848
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Heo L, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.797
2016 Heo L, Lee H, Baek M, Seok C. Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers. Methods in Molecular Biology (Clifton, N.J.). 1414: 33-45. PMID 27094284 DOI: 10.1007/978-1-4939-3569-7_3  0.82
2015 Lee GR, Heo L, Seok C. Effective protein model structure refinement by loop modeling and overall relaxation. Proteins. 293-301. PMID 26172288 DOI: 10.1002/prot.24858  0.847
2015 Lee KL, Singh AK, Heo L, Seok C, Roe JH. Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds. Molecular Microbiology. PMID 25998932 DOI: 10.1111/Mmi.13068  0.522
2015 Lee H, Heo L, Lee MS, Seok C. GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization. Nucleic Acids Research. PMID 25969449 DOI: 10.1093/nar/gkv495  0.832
2014 Park H, Lee GR, Heo L, Seok C. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. Plos One. 9: e113811. PMID 25419655 DOI: 10.1371/journal.pone.0113811  0.838
2014 Heo L, Shin WH, Lee MS, Seok C. GalaxySite: ligand-binding-site prediction by using molecular docking. Nucleic Acids Research. 42: W210-4. PMID 24753427 DOI: 10.1093/nar/gku321  0.795
2014 Kim Y, Lee H, Heo L, Seok C, Choe J. Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif. Protein Science : a Publication of the Protein Society. 23: 906-14. PMID 24723367 DOI: 10.1002/Pro.2472  0.784
2013 Heo L, Park H, Seok C. GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Research. 41: W384-8. PMID 23737448 DOI: 10.1093/nar/gkt458  0.839
2013 Heo L, Cho YB, Lee MS, Roe JH, Seok C. Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors. Proteins. 81: 1644-52. PMID 23670838 DOI: 10.1002/Prot.24323  0.632
2013 Kim MS, Lee H, Heo L, Lim A, Seok C, Shin DH. New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies. Proteins. 81: 1499-508. PMID 23483653 DOI: 10.1002/prot.24275  0.782
2012 Ko J, Park H, Heo L, Seok C. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research. 40: W294-7. PMID 22649060 DOI: 10.1093/nar/gks493  0.846
2011 Shin WH, Heo L, Lee J, Ko J, Seok C, Lee J. LigDockCSA: protein-ligand docking using conformational space annealing. Journal of Computational Chemistry. 32: 3226-32. PMID 21837636 DOI: 10.1002/jcc.21905  0.773
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