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Minkyung Baek - Publications

Affiliations: 
Seoul National University, Seoul, South Korea 
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39 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 Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nature Microbiology. PMID 39294458 DOI: 10.1038/s41564-024-01791-x  0.491
2024 Sledzieski S, Kshirsagar M, Baek M, Dodhia R, Lavista Ferres J, Berger B. Democratizing protein language models with parameter-efficient fine-tuning. Proceedings of the National Academy of Sciences of the United States of America. 121: e2405840121. PMID 38900798 DOI: 10.1073/pnas.2405840121  0.38
2024 Kshirsagar M, Meller A, Humphreys I, Sledzieski S, Xu Y, Dodhia R, Horvitz E, Berger B, Bowman G, Ferres JL, Baker D, Baek M. Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm. Research Square. PMID 38746169 DOI: 10.21203/rs.3.rs-4215086/v1  0.55
2024 Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Essential and virulence-related protein interactions of pathogens revealed through deep learning. Biorxiv : the Preprint Server For Biology. PMID 38645026 DOI: 10.1101/2024.04.12.589144  0.483
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  0.815
2024 Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, ... ... Baek M, et al. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science (New York, N.Y.). eadl2528. PMID 38452047 DOI: 10.1126/science.adl2528  0.772
2023 Baek M, McHugh R, Anishchenko I, Jiang H, Baker D, DiMaio F. Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA. Nature Methods. PMID 37996753 DOI: 10.1038/s41592-023-02086-5  0.512
2023 Sledzieski S, Kshirsagar M, Baek M, Berger B, Dodhia R, Ferres JL. Democratizing Protein Language Models with Parameter-Efficient Fine-Tuning. Biorxiv : the Preprint Server For Biology. PMID 37986761 DOI: 10.1101/2023.11.09.566187  0.344
2023 Mansoor S, Baek M, Juergens D, Watson JL, Baker D. Zero-shot Mutation Effect Prediction on Protein Stability and Function using RoseTTAFold. Protein Science : a Publication of the Protein Society. e4780. PMID 37695922 DOI: 10.1002/pro.4780  0.457
2023 Watson JL, Juergens D, Bennett NR, Trippe BL, Yim J, Eisenach HE, Ahern W, Borst AJ, Ragotte RJ, Milles LF, Wicky BIM, Hanikel N, Pellock SJ, Courbet A, Sheffler W, ... ... Baek M, et al. De novo design of protein structure and function with RFdiffusion. Nature. PMID 37433327 DOI: 10.1038/s41586-023-06415-8  0.446
2023 Bennett NR, Coventry B, Goreshnik I, Huang B, Allen A, Vafeados D, Peng YP, Dauparas J, Baek M, Stewart L, DiMaio F, De Munck S, Savvides SN, Baker D. Improving de novo protein binder design with deep learning. Nature Communications. 14: 2625. PMID 37149653 DOI: 10.1038/s41467-023-38328-5  0.324
2023 MacRae MR, Puvanendran D, Haase MAB, Coudray N, Kolich L, Lam C, Baek M, Bhabha G, Ekiert DC. Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning. The Journal of Biological Chemistry. 104744. PMID 37100290 DOI: 10.1016/j.jbc.2023.104744  0.368
2023 Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, ... ... Baek M, et al. Top-down design of protein architectures with reinforcement learning. Science (New York, N.Y.). 380: 266-273. PMID 37079676 DOI: 10.1126/science.adf6591  0.322
2023 Motmaen A, Dauparas J, Baek M, Abedi MH, Baker D, Bradley P. Peptide-binding specificity prediction using fine-tuned protein structure prediction networks. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216697120. PMID 36802421 DOI: 10.1073/pnas.2216697120  0.447
2022 Wang J, Lisanza S, Juergens D, Tischer D, Watson JL, Castro KM, Ragotte R, Saragovi A, Milles LF, Baek M, Anishchenko I, Yang W, Hicks DR, Expòsit M, Schlichthaerle T, et al. Scaffolding protein functional sites using deep learning. Science (New York, N.Y.). 377: 387-394. PMID 35862514 DOI: 10.1126/science.abn2100  0.441
2022 Baek M, Baker D. Deep learning and protein structure modeling. Nature Methods. 19: 13-14. PMID 35017724 DOI: 10.1038/s41592-021-01360-8  0.389
2021 Humphreys IR, Pei J, Baek M, Krishnakumar A, Anishchenko I, Ovchinnikov S, Zhang J, Ness TJ, Banjade S, Bagde SR, Stancheva VG, Li XH, Liu K, Zheng Z, Barrero DJ, et al. Computed structures of core eukaryotic protein complexes. Science (New York, N.Y.). eabm4805. PMID 34762488 DOI: 10.1126/science.abm4805  0.382
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  0.763
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  0.777
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  0.835
2021 Park T, Won J, Baek M, Seok C. GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking. Nucleic Acids Research. PMID 34048578 DOI: 10.1093/nar/gkab422  0.844
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  0.789
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  0.706
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  0.835
2019 Park T, Woo H, Baek M, Yang J, Seok C. Structure Prediction of Biological Assemblies using GALAXY in CAPRI Rounds 38-45. Proteins. PMID 31774573 DOI: 10.1002/prot.25859  0.811
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Baek M, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.809
2019 Baek M, Park T, Woo H, Seok C. Prediction of Protein Oligomer Structures using GALAXY in CASP13. Proteins. PMID 31509276 DOI: 10.1002/prot.25814  0.849
2019 Won J, Baek M, Monastyrskyy B, Kryshtafovych A, Seok C. Assessment of Protein Model Structure Accuracy Estimation in CASP13: Challenges in the Era of Deep Learning. Proteins. PMID 31436360 DOI: 10.1002/prot.25804  0.826
2019 Yang J, Baek M, Seok C. GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility. Journal of Computational Chemistry. PMID 31423613 DOI: 10.1002/jcc.26050  0.802
2019 Park T, Baek M, Lee H, Seok C. GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters. Journal of Computational Chemistry. PMID 31173387 DOI: 10.1002/jcc.25874  0.824
2018 Oh SH, Sung YH, Kim I, Sim CK, Lee JH, Baek M, Pack CG, Seok C, Seo EJ, Lee MS, Kim KM. Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease. Inflammatory Bowel Diseases. PMID 30462267 DOI: 10.1093/ibd/izy353  0.512
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  0.843
2017 Baek M, Shin WH, Chung HW, Seok C. GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking. Journal of Computer-Aided Molecular Design. PMID 28623486 DOI: 10.1007/s10822-017-0030-9  0.801
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  0.86
2016 Lee H, Baek M, Lee GR, Park S, Seok C. Template-based Modeling and Ab Initio Refinement of Protein Oligomer Structures using GALAXY in CAPRI Round 30. Proteins. PMID 27770545 DOI: 10.1002/prot.25192  0.843
2016 Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR. Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. Journal of Computer-Aided Molecular Design. PMID 27696242 DOI: 10.1007/S10822-016-9965-5  0.734
2016 Lee J, Tofoleanu F, Pickard FC, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. Journal of Computer-Aided Molecular Design. PMID 27677749 DOI: 10.1007/S10822-016-9968-2  0.704
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, 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  0.83
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  0.834
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