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Hahnbeom Park - Publications

Affiliations: 
Seoul National University, Seoul, South Korea 
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41/47 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
2024 Mansoor S, Baek M, Park H, Lee GR, Baker D. Protein Ensemble Generation Through Variational Autoencoder Latent Space Sampling. Journal of Chemical Theory and Computation. PMID 38547871 DOI: 10.1021/acs.jctc.3c01057  0.818
2023 Choi C, Bae J, Kim S, Lee S, Kang H, Kim J, Bang I, Kim K, Huh WK, Seok C, Park H, Im W, Choi HJ. Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family. Nature Communications. 14: 8105. PMID 38062020 DOI: 10.1038/s41467-023-43983-9  0.78
2023 Lee S, Seok C, Park H. Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design. Journal of Computational Chemistry. PMID 36847771 DOI: 10.1002/jcc.27091  0.831
2022 Lee S, Kim S, Lee GR, Kwon S, Woo H, Seok C, Park H. Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction. Computational and Structural Biotechnology Journal. 21: 158-167. PMID 36544468 DOI: 10.1016/j.csbj.2022.11.057  0.778
2021 Anishchenko I, Baek M, Park H, Hiranuma N, Kim DE, Dauparas J, Mansoor S, Humphreys IR, Baker D. Protein tertiary structure prediction and refinement using deep learning and Rosetta in CASP14. Proteins. PMID 34331359 DOI: 10.1002/prot.26194  0.773
2021 Baek M, Anishchenko I, Park H, Humphreys IR, Baker D. Protein oligomer modeling guided by predicted inter-chain contacts in CASP14. Proteins. PMID 34324224 DOI: 10.1002/prot.26197  0.781
2021 Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.). PMID 34282049 DOI: 10.1126/science.abj8754  0.827
2021 Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nature Communications. 12: 1340. PMID 33637700 DOI: 10.1038/s41467-021-21511-x  0.802
2021 Park H, Zhou G, Baek M, Baker D, DiMaio F. Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking. Journal of Chemical Theory and Computation. PMID 33577321 DOI: 10.1021/acs.jctc.0c01184  0.731
2020 Pavlovicz RE, Park H, DiMaio F. Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination. Plos Computational Biology. 16: e1008103. PMID 32956350 DOI: 10.1371/Journal.Pcbi.1008103  0.412
2020 Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences of the United States of America. PMID 31896580 DOI: 10.1073/Pnas.1914677117  0.576
2019 Park H, Lee GR, Kim DE, Anishchanka I, Cong Q, Baker D. High-accuracy refinement using Rosetta in CASP13. Proteins. PMID 31325340 DOI: 10.1002/Prot.25784  0.773
2018 Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, et al. De novo design of a fluorescence-activating β-barrel. Nature. PMID 30209393 DOI: 10.1038/S41586-018-0509-0  0.323
2018 Won J, Lee GR, Park H, Seok C. GalaxyGPCRloop: Template-based and Ab Initio Structure Sampling of the Extracellular Loops of G-protein-coupled Receptors. Journal of Chemical Information and Modeling. PMID 29786430 DOI: 10.1021/acs.jcim.8b00148  0.806
2018 Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D. Protein homology model refinement by large-scale energy optimization. Proceedings of the National Academy of Sciences of the United States of America. PMID 29507254 DOI: 10.1073/Pnas.1719115115  0.392
2017 Dou J, Doyle L, Greisen PJ, Schena A, Park H, Johnsson K, Stoddard BL, Baker D. Sampling and Energy Evaluation Challenges in Ligand Binding Protein Design. Protein Science : a Publication of the Protein Society. PMID 28980354 DOI: 10.1002/Pro.3317  0.317
2017 Ovchinnikov S, Park H, Kim D, DiMaio F, Baker D. Protein structure prediction using Rosetta in CASP12. Proteins. PMID 28940798 DOI: 10.1002/Prot.25390  0.538
2017 Park H, Kim D, Ovchinnikov S, Baker D, DiMaio F. Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins. PMID 28913931 DOI: 10.1002/Prot.25387  0.493
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.338
2017 Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science (New York, N.Y.). 355: 294-298. PMID 28104891 DOI: 10.1126/Science.Aah4043  0.482
2016 Park H, Bradley P, Greisen P, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F. Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules. Journal of Chemical Theory and Computation. PMID 27766851 DOI: 10.1021/Acs.Jctc.6B00819  0.446
2016 Ovchinnikov S, Park H, Kim DE, Liu Y, Yu-Ruei Wang R, Baker D. Structure Prediction using sparse simulated NOE restraints with Rosetta in CASP11. Proteins. PMID 26857542 DOI: 10.1002/Prot.25006  0.422
2015 Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large scale determination of previously unsolved protein structures using evolutionary information. Elife. 4. PMID 26335199 DOI: 10.7554/Elife.09248  0.55
2015 Park H, Lee H, Seok C. High-resolution protein-protein docking by global optimization: recent advances and future challenges. Current Opinion in Structural Biology. 35: 24-31. PMID 26295792 DOI: 10.1016/j.sbi.2015.08.001  0.828
2015 Park H, DiMaio F, Baker D. CASP11 refinement experiments with ROSETTA. Proteins. PMID 26205421 DOI: 10.1002/Prot.24862  0.464
2015 Park H, DiMaio F, Baker D. The origin of consistent protein structure refinement from structural averaging. Structure (London, England : 1993). 23: 1123-8. PMID 25960407 DOI: 10.1016/J.Str.2015.03.022  0.455
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  0.848
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Park H, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.789
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Park H, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.805
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  0.846
2013 Lee H, Park H, Ko J, Seok C. GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity. Bioinformatics (Oxford, England). 29: 1078-80. PMID 23413437 DOI: 10.1093/bioinformatics/btt079  0.831
2012 Ko J, Park H, Seok C. GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. Bmc Bioinformatics. 13: 198. PMID 22883815 DOI: 10.1186/1471-2105-13-198  0.842
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  0.848
2012 Park H, Seok C. Refinement of unreliable local regions in template-based protein models. Proteins. 80: 1974-86. PMID 22488760 DOI: 10.1002/prot.24086  0.717
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.788
2011 Choi J, Park H, Seok C. How does a registry change in dynein's coiled-coil stalk drive binding of dynein to microtubules? Biochemistry. 50: 7629-36. PMID 21809817 DOI: 10.1021/bi200834k  0.722
2011 Park H, Ko J, Joo K, Lee J, Seok C, Lee J. Refinement of protein termini in template-based modeling using conformational space annealing. Proteins. 79: 2725-34. PMID 21755541 DOI: 10.1002/prot.23101  0.848
2011 Park H, Im W, Seok C. Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. Biophysical Journal. 100: 2955-63. PMID 21689529 DOI: 10.1016/J.Bpj.2011.05.030  0.588
2011 Ko J, Lee D, Park H, Coutsias EA, Lee J, Seok C. The FALC-Loop web server for protein loop modeling. Nucleic Acids Research. 39: W210-4. PMID 21576220 DOI: 10.1093/Nar/Gkr352  0.83
2010 Lee J, Lee D, Park H, Coutsias EA, Seok C. Protein loop modeling by using fragment assembly and analytical loop closure. Proteins. 78: 3428-36. PMID 20872556 DOI: 10.1002/Prot.22849  0.803
2008 Park H, Yoon J, Seok C. Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins. The Journal of Physical Chemistry. B. 112: 1041-8. PMID 18154287 DOI: 10.1021/jp077285n  0.594
Low-probability matches (unlikely to be authored by this person)
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Park H, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.283
2020 Frenz B, Lewis SM, King I, DiMaio F, Park H, Song Y. Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy. Frontiers in Bioengineering and Biotechnology. 8: 558247. PMID 33134287 DOI: 10.3389/fbioe.2020.558247  0.223
2022 Kim DI, Han SH, Park H, Choi S, Kaur M, Hwang E, Han SJ, Ryu JY, Cheong HK, Barnwal RP, Lim YB. Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets. Journal of the American Chemical Society. PMID 35972994 DOI: 10.1021/jacs.2c03858  0.214
2022 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500  0.174
2021 Falekun S, Sepulveda J, Jami-Alahmadi Y, Park H, Wohlschlegel JA, Sigala PA. Divergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasites. Elife. 10. PMID 34612205 DOI: 10.7554/eLife.71636  0.096
2023 Baek SY, Lee J, Kim T, Lee H, Choi HS, Park H, Koh M, Kim E, Jung ME, Iliopoulos D, Lee JY, Kim J, Lee S. Development of a novel histone deacetylase inhibitor unveils the role of HDAC11 in alleviating depression by inhibition of microglial activation. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie. 166: 115312. PMID 37567072 DOI: 10.1016/j.biopha.2023.115312  0.049
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