| 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 |
0.403 |
|
| 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 |
0.778 |
|
| 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 |
0.828 |
|
| 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 |
0.775 |
|
| 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 |
0.778 |
|
| 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 |
0.786 |
|
| 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 |
0.825 |
|
| 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 |
0.806 |
|
| 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 |
0.733 |
|
| 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 |
0.413 |
|
| 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 |
0.579 |
|
| 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 |
0.776 |
|
| 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 |
0.324 |
|
| 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 |
0.802 |
|
| 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 |
0.395 |
|
| 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 |
0.54 |
|
| 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 |
0.496 |
|
| 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 |
0.34 |
|
| 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 |
0.483 |
|
| 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 |
0.448 |
|
| 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 |
0.425 |
|
| 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 |
0.827 |
|
| 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 |
0.847 |
|
| 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 |
0.845 |
|
| 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 |
0.829 |
|
| 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 |
0.847 |
|
| 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 |
0.721 |
|
| 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 |
0.787 |
|
| 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 |
0.721 |
|
| 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 |
0.595 |
|
| Show low-probability matches. |