Publications: Applications and collaborations
CASP and CAPRI collaborations
- J. Won1, M. Baek1, B. Monastyrskyy, A. Kryshtafovych, and C. Seok*,
Assessment of Protein Model Structure Accuracy Estimation in CASP13: Challenges in the Era of Deep Learning,
Proteins: Structure, Function, and Bioinformatics, 87 (12), 1350-1360 (2019). 1Co-first authors
- M. Lensink et al. (M. Baek, T. Park, H. Woo, and C. Seok),
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment,
Proteins: Structure, Function, and Bioinformatics, 87 (12), 1200-1221 (2019).
- C. Keasar et al. (L. Heo, G. R. Lee, C. Seok)
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12,
Sci. Rep., 8:9939 (2018).
- M. F. Lensink*, S. Velankar, M. Baek, L. Heo, C. Seok, and S. J. Wodak*,
The challenge of modeling protein assemblies: the CASP12-CAPRI experiment,
Proteins: Structure, Function, and Bioinformatics, 86 (S1), 257-273 (2018).
- M. F. Lensik et al. (H. Lee, M. Baek, S. Park, L. Heo, G. R. Lee, C. Seok),
Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment,
Proteins: Structure, Function, and Bioinformatics, 84 (S1), 323-348 (2016).
- M. F. Lensink et al. (H, Park, J. Ko, H. Lee, C. Seok), Blind prediction of interfacial water positions in CAPRI, Proteins: Structure, Function, and Bioinformatics, 82 (4), 620-632 (2014).
- R. Moretti et al. (H. Lee, H, Park, C. Seok), Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Proteins: Structure, Function, and Bioinformatics, 81 (11), 1980-1987 (2013).
- Sarel J Fleishman et al. (H. Park, J. Ko, H. Lee, C. Seok), Community-wide assessment of protein-interface modeling suggests improvements to design methodology, J. Mol. Biol. 414 (2), 289-302 (2011).
Collaborations in other competitions
- Q. Xu, Q. Tang, P. Katsonis, O. Lichtarge, D. T. Jones, S. Bovo, G. Babbi, P. L. Martelli, R. Casadio, G. R. LEE, C. Seok, A. Fenton*, R. L. Dunbrack, Jr*,
Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4,
Human Mutation. 38 (9), 1123-1131 (2017).
- F. Tofoleanu*, J. Lee, F. C. Pickard IV, G. König, J. Huang, M. Baek, C. Seok, and B. Brooks,
Absolute binding free energies for octa-acids and guests in SAMPL5,
J. Comput. Aid. Mol. Design, 31 (1), 107-118 (2017).
- J. Lee*, F. Tofoleanu, F. C. Pickard IV, G. König, J. Huang, A. Damjanović, M. Baek, C. Seok, and B. Brooks,
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge,
J. Comput. Aid. Mol. Design, 31 (1), 71-85 (2017).
- Y. K. Choi, Y. Cao, M. Frank, H. Woo, S. J. Park, M. S. Yeom, T. I. Croll, C. Seok, and W. Im*,
Sturcture, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycoslyated Full-Length SARS-CoV-2
Spike Protein in a Viral Membrane, J. Chem. Theory Comput., 17 (4), 2479-2487 (2021).
- H. Woo1, S.-J. Park1, Y. K. Choi1, T. Park, M. Tanveer, Y. Cao, N. R. Kern, J. Lee, M. S. Yeom, T. I. Croll*, C. Seok*, and W. Im*,
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane,
J. Phys. Chem. B, 124 (33), 7128-7137 (2020). 1Co-first authors
- H. S. Lee, C. Seok, and W. Im*, Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy, J. Chem. Theo. Comput. 11 (3), 1255-1266 (2015).
- H. Park, W. Im, and C. Seok*, Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies, Biophys. J. 100, 2955-2963 (2011).
- J. Lee, Y. -G. Kim, K. K. Kim, and C. Seok*, Transition between B-DNA and Z-DNA: Free Energy Landscape for the B-Z Junction Propagation, J. Phys. Chem. B, 114, 9872-9881 (2010).
- J. Lee, J. Kim, and C. Seok*, Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: A molecular dynamics simulation study, J. Phys. Chem. B, 114, 7662-7671 (2010).
- S. Kang, J. Lee, M. S. Lee, and C. Seok*, Structural basis of functional conversion of a floral repressor to an activator, Bull. Korean Chem. Soc. 29, 408 (2008).
- J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations, J. Chem. Theo. Comput. 3, 26-41 (2007).
Collaborations with experimentalists
- J. Yu, J. Yang, C. Seok, W. J. Song*,
Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes,
Chemical Science, 12 (14), 5091-5101 (2021).
- J. Kim, W. Han, T. Park, ..., C. Seok, J.-K. Han, and H.-J. Choi*,
Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains,
Nat Commun, 11, 5357 (2020).
- G. Kim, J. Yang, J. Jang, J.-S. Choi, A. J. Roe, O. Byron, C. Seok, and J.-J. Song*,
Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling,
Commun. Biol, 3, 298 (2020).
- T. D. Ngo, C. Oh, P. Mizar, M. Baek, K. Park, L. Nguyen, H. Byeon, S. Yoon, Y. Ryu, B. H. Ryu, T. D. Kim, J. W. Yang, C. Seok, S. S. Lee, and K. K. Kim*,
Structural Basis for the Enantioselectivity of Esterase Est-Y29 toward (S)-Ketoprofen,
ACS Catalysis, 9, 755-767 (2019).
- S. H. Oh*, Y. H. Sung, I. Kim, C. K. Sim, J. H. Lee, M. Baek, C.-G. Pack, C. Seok, E. J. Seo, M. S. Lee*, and K. M. Kim,
Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease,
Inflamm Bowel Dis, 25, 498-509 (2019).
- I. Bang1, H. R. Kim1, A. H. Beaven, J. Kim, S. Ko, G. R. Lee, H. Lee, W. Im, C. Seok, K. Y. Chung*, H.-J. Choi*,
Biophysical and functional characterization of Norrin signaling through Frizzled4,
Proc. Natl. Acad. Sci., 115 (35), 8787-8792 (2018). 1Co-first authors
- X. Shao1, H. Kang1, T. Loveless, G. R. Lee, C. Seok, W. I. Weis, H.-J. Choi*, and J. Hardin*,
Structural and functional characterization of the α-catenin⋅β-catenin binding interface
in Caenorhabditis elegans reveals conserved requirements for cell-cell adhesion in metazoans,
J. Biol. Chem. 292, 16477. (2017). 1Co-first authors
- D. Ka, H. Lee, Y.-D. Jung, K. Kim, C. Seok, N. Suh, and E. Bae*, Crystal structure of Streptococcus pyogenes Cas1 and its interaction with Csn2 in the type II CRISPR-Cas system, Structure, 24 (1), 70-79 (2016).
- K. -L. Lee, A. K. Singh, L. Heo, C. Seok, and J. -H. Roe*, Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds, Mol. Microbiol., 97 (5), 808-821 (2015).
- S. Lee, W. -H. Shin, S. Hong, H. B. Kang, D. Jung, U. H. Yim, W. J. Shim, J. S. Khim, C. Seok, J. P. Giesy, and K. Choi*, Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues, Chemosphere, 139, 23-29 (2015).
- Y. Kim, H. Lee, L. Heo, C. Seok, and J. Choe*, Structure of Vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif, Protein Science, 23 (7), 906-914 (2014).
- Y. Kim, S. Shin, T. Kim, D. Lee, C. Seok, and M. Lee*, Switchable nanoporous sheets by the aqueous self-assembly of aromatic macrobicycles, Angew. Chem. Int. Ed., 52 (25), 6426-6429 (2013).
- M.-S. Kim, H. Lee, A. Lim, L. Heo, C. Seok*, and D. H. Shin*, New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies, Proteins: Structure, Function, and Bioinformatics, 81 (9), 1499-1508 (2013).
- Z. Huang, S. -K. Kang, M. Banno, T. Yanaguchi, D. Lee, C. Seok, E. Yashima, and M. Lee*, Pulsating tubules from noncovalent macrocyles, Science, 337 (6101), 1521-1526 (2012).
- J. Ham, et al, Discovery, design and synthesis of Y-shaped peroxisome proliferator-activated receptor d agonists as potent anti-obesity agents in vivo, Eur. J. Med. Chem. 53, 190-202 (2012).
- H. -J. Kim, S. -K. Kang, Y. -K. Lee, C. Seok, J. -K. Lee, W. -C. Zin, and M. Lee*, Self-Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles, Angew. Chem. Int. Ed. 122, 8649-1653 (2010).
- D. Lee, J. Lee, and C. Seok*, What stabilizes close arginine pairing in proteins?, Phys. Chem. Chem. Phys., 15 (16), 5844-5853 (2013).
- Y.-K. Lee, J. Lee, J. H. Choi, and C. Seok*, Contribution of counterion entropy to the salt-induced transition between B-DNA and Z-DNA, Bull. Korean Chem. Soc. 33, 3719-3726 (2012).
- J. Choi, H. Park, and C. Seok*, How does registry change of dynein's coiled-coil stalk drive binding of dynein to microtubule?, Biochemistry, 50 (35), 7629-7636 (2011).
- J. Lee, J. Lee, T. N. Sasaki, M. Sasai, C. Seok*, and J. Lee*, De novo protein structure prediction by dynamic fragment assembly and conformational space annealing, Proteins: Structure, Function, and Bioinformatics, 79, 2403-2417 (2011).
- H. Park, J. Yoon, and C. Seok*, Strength of Ca-H...O=C Hydrogen Bonds in Transmembrane Proteins, J. Phys. Chem. B, 112, 1041-1048 (2008).