| Year |
Citation |
Score |
| 2025 |
Kshirsagar M, Meller A, Humphreys IR, Sledzieski S, Xu Y, Dodhia R, Horvitz E, Berger B, Bowman GR, Ferres JL, Baker D, Baek M. Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm. Nature Communications. 16: 2017. PMID 40016259 DOI: 10.1038/s41467-025-57148-3 |
0.553 |
|
| 2025 |
Park S, Myung S, Baek M. Advancing protein structure prediction beyond AlphaFold2. Current Opinion in Structural Biology. 90: 102985. PMID 39862760 DOI: 10.1016/j.sbi.2025.102985 |
0.539 |
|
| 2025 |
Yoon MS, Bae B, Kim K, Park H, Baek M. Deep learning methods for proteome-scale interaction prediction. Current Opinion in Structural Biology. 90: 102981. PMID 39848140 DOI: 10.1016/j.sbi.2024.102981 |
0.743 |
|
| 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 |
0.496 |
|
| 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 |
0.382 |
|
| 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 |
0.552 |
|
| 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 |
0.487 |
|
| 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 |
0.812 |
|
| 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 |
0.764 |
|
| 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 |
0.513 |
|
| 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 |
0.345 |
|
| 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 |
0.325 |
|
| 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 |
0.367 |
|
| 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 |
0.326 |
|
| 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 |
0.446 |
|
| 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 |
0.443 |
|
| 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 |
0.394 |
|
| 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 |
0.76 |
|
| 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 |
0.775 |
|
| 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 |
0.833 |
|
| 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 |
0.787 |
|
| 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 |
0.701 |
|
| 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 |
0.834 |
|
| 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 |
0.813 |
|
| 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 |
0.804 |
|
| 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 |
0.825 |
|
| 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 |
0.507 |
|
| 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 |
0.842 |
|
| 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 |
0.796 |
|
| 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 |
0.844 |
|
| 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 |
0.728 |
|
| 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 |
0.698 |
|
| 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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