| Year |
Citation |
Score |
| 2024 |
Kwon S, Jung N, Yang J, Seok C. GalaxySagittarius-AF: Predicting Targets for Drug-Like Compounds in the Extended Human 3D Proteome. Journal of Molecular Biology. 436: 168617. PMID 39237198 DOI: 10.1016/j.jmb.2024.168617 |
0.841 |
|
| 2024 |
Lee C, Won J, Ryu S, Yang J, Jung N, Park H, Seok C. GalaxyDock-DL: Protein-Ligand Docking by Global Optimization and Neural Network Energy. Journal of Chemical Theory and Computation. PMID 39109987 DOI: 10.1021/acs.jctc.4c00385 |
0.825 |
|
| 2024 |
Woo H, Kim Y, Seok C. Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. Plos Computational Biology. 20: e1012239. PMID 38913733 DOI: 10.1371/journal.pcbi.1012239 |
0.841 |
|
| 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 |
0.804 |
|
| 2023 |
Choi WH, Yun Y, Byun I, Kim S, Lee S, Sim J, Levi S, Park SH, Jun J, Kleifeld O, Kim KP, Han D, Chiba T, Seok C, Kwon YT, et al. ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation. Cell Reports. 42: 112701. PMID 37384533 DOI: 10.1016/j.celrep.2023.112701 |
0.768 |
|
| 2023 |
Seo J, Park M, Ko D, Kim S, Park JM, Park S, Nam KD, Farrand L, Yang J, Seok C, Jung E, Kim YJ, Kim JY, Seo JH. Ebastine impairs metastatic spread in triple-negative breast cancer by targeting focal adhesion kinase. Cellular and Molecular Life Sciences : Cmls. 80: 132. PMID 37185776 DOI: 10.1007/s00018-023-04760-5 |
0.756 |
|
| 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 |
0.838 |
|
| 2023 |
Lee C, Yang J, Kwon S, Seok C. GalaxyDock2-HEME: Protein-ligand docking for heme proteins. Journal of Computational Chemistry. PMID 36809651 DOI: 10.1002/jcc.27092 |
0.814 |
|
| 2022 |
Lee J, Seok C, Ham S, Chong SH. Atomic-Level Thermodynamics Analysis of the Binding Free Energy of SARS-CoV-2 Neutralizing Antibodies. Proteins. PMID 36564921 DOI: 10.1002/prot.26458 |
0.663 |
|
| 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 |
0.834 |
|
| 2022 |
Kang H, Park C, Choi YK, Bae J, Kwon S, Kim J, Choi C, Seok C, Im W, Choi HJ. Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling. Structure (London, England : 1993). PMID 36525977 DOI: 10.1016/j.str.2022.11.010 |
0.689 |
|
| 2022 |
Kwon S, Seok C. CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking. Computational and Structural Biotechnology Journal. 21: 1-10. PMID 36514334 DOI: 10.1016/j.csbj.2022.11.047 |
0.776 |
|
| 2022 |
Sim J, Kwon S, Seok C. HProteome-BSite: predicted binding sites and ligands in human 3D proteome. Nucleic Acids Research. PMID 36243970 DOI: 10.1093/nar/gkac873 |
0.84 |
|
| 2022 |
Park S, Seok C. GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. Journal of Chemical Information and Modeling. PMID 35749367 DOI: 10.1021/acs.jcim.2c00306 |
0.61 |
|
| 2022 |
Choi J, Park T, Yul Lee S, Yang J, Seok C. GalaxyDomDock: An Ab Initio Domain-domain Docking Web Server for Multi-domain Protein Structure Prediction. Journal of Molecular Biology. 434: 167508. PMID 35662464 DOI: 10.1016/j.jmb.2022.167508 |
0.798 |
|
| 2022 |
Park C, Kim J, Ko SB, Choi YK, Jeong H, Woo H, Kang H, Bang I, Kim SA, Yoon TY, Seok C, Im W, Choi HJ. Author Correction: Structural basis of neuropeptide Y signaling through Y1 receptor. Nature Communications. 13: 1126. PMID 35217654 DOI: 10.1038/s41467-022-28837-0 |
0.758 |
|
| 2022 |
Park C, Kim J, Ko SB, Choi YK, Jeong H, Woo H, Kang H, Bang I, Kim SA, Yoon TY, Seok C, Im W, Choi HJ. Structural basis of neuropeptide Y signaling through Y1 receptor. Nature Communications. 13: 853. PMID 35165283 DOI: 10.1038/s41467-022-28510-6 |
0.79 |
|
| 2022 |
Kim J, Han W, Park T, Kim EJ, Bang I, Lee HS, Jeong Y, Roh K, Kim J, Kim JS, Kang C, Seok C, Han JK, Choi HJ. Author Correction: Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature Communications. 13: 738. PMID 35110580 DOI: 10.1038/s41467-022-28394-6 |
0.558 |
|
| 2022 |
Heo K, Lee JW, Jang Y, Kwon S, Lee J, Seok C, Ha NC, Seok YJ. A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae. The Journal of Biological Chemistry. 101626. PMID 35074425 DOI: 10.1016/j.jbc.2022.101626 |
0.651 |
|
| 2021 |
Kang B, Seok C, Lee J. MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization. Acs Omega. 6: 27454-27465. PMID 34693166 DOI: 10.1021/acsomega.1c04347 |
0.766 |
|
| 2021 |
Cao Y, Choi YK, Frank M, Woo H, Park SJ, Yeom MS, Seok C, Im W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Journal of Chemical Theory and Computation. PMID 34529436 DOI: 10.1021/acs.jctc.1c00552 |
0.776 |
|
| 2021 |
Ohn J, Been KW, Kim JY, Kim EJ, Park T, Yoon HJ, Ji JS, Okada-Iwabu M, Iwabu M, Yamauchi T, Kim YK, Seok C, Kwon O, Kim KH, Lee HH, et al. Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth. Embo Molecular Medicine. e13790. PMID 34486824 DOI: 10.15252/emmm.202013790 |
0.601 |
|
| 2021 |
Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J. Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins. PMID 34462960 DOI: 10.1002/prot.26231 |
0.844 |
|
| 2021 |
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, ... ... Seok C, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins. PMID 34453465 DOI: 10.1002/prot.26222 |
0.811 |
|
| 2021 |
Park T, Woo H, Yang J, Kwon S, Won J, Seok C. Protein Oligomer Structure Prediction using GALAXY in CASP14. Proteins. PMID 34363243 DOI: 10.1002/prot.26203 |
0.847 |
|
| 2021 |
Kwon S, Won J, Kryshtafovych A, Seok C. Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges. Proteins. PMID 34324227 DOI: 10.1002/prot.26192 |
0.828 |
|
| 2021 |
Yu J, Yang J, Seok C, Song WJ. Symmetry-related residues as promising hotspots for the evolution of oligomeric enzymes. Chemical Science. 12: 5091-5101. PMID 34168770 DOI: 10.1039/d0sc06823c |
0.809 |
|
| 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 |
0.864 |
|
| 2021 |
Cao Y, Choi YK, Frank M, Woo H, Park SJ, Yeom MS, Seok C, Im W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Biorxiv : the Preprint Server For Biology. PMID 34013268 DOI: 10.1101/2021.05.10.443519 |
0.776 |
|
| 2021 |
Heo L, Park S, Seok C. GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. Journal of Chemical Information and Modeling. PMID 33938216 DOI: 10.1021/acs.jcim.0c01434 |
0.794 |
|
| 2021 |
Choi YK, Cao Y, Frank M, Woo H, Park SJ, Yeom MS, Croll TI, Seok C, Im W. Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of Chemical Theory and Computation. PMID 33689337 DOI: 10.1021/acs.jctc.0c01144 |
0.808 |
|
| 2020 |
Kim J, Han W, Park T, Kim EJ, Bang I, Lee HS, Jeong Y, Roh K, Kim J, Kim JS, Kang C, Seok C, Han JK, Choi HJ. Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature Communications. 11: 5357. PMID 33097721 DOI: 10.1038/s41467-020-19155-4 |
0.628 |
|
| 2020 |
Kang B, Seok C, Lee J. Prediction of Molecular Electronic Transitions Using Random Forests. Journal of Chemical Information and Modeling. PMID 33090804 DOI: 10.1021/acs.jcim.0c00698 |
0.778 |
|
| 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 |
0.844 |
|
| 2020 |
Woo H, Park SJ, Choi YK, Park T, Tanveer M, Cao Y, Kern NR, Lee J, Yeom MS, Croll TI, Seok C, Im W. Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane. The Journal of Physical Chemistry. B. PMID 32559081 DOI: 10.1021/Acs.Jpcb.0C04553 |
0.828 |
|
| 2020 |
Kim G, Yang J, Jang J, Choi JS, Roe AJ, Byron O, Seok C, Song JJ. Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling. Communications Biology. 3: 298. PMID 32523125 DOI: 10.1038/s42003-020-1030-1 |
0.787 |
|
| 2020 |
Woo H, Park SJ, Choi YK, Park T, Tanveer M, Cao Y, Kern NR, Lee J, Yeom MS, Croll T, Seok C, Im W. Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane. Biorxiv : the Preprint Server For Biology. PMID 32511389 DOI: 10.1101/2020.05.20.103325 |
0.826 |
|
| 2020 |
Yang J, Kwon S, Bae SH, Park KM, Yoon C, Lee JH, Seok C. GalaxySagittarius: Structure- and similarity-based prediction of protein targets for drug-like compounds. Journal of Chemical Information and Modeling. PMID 32401021 DOI: 10.1021/acs.jcim.0c00104 |
0.853 |
|
| 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 |
0.847 |
|
| 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, ... ... Seok C, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838 |
0.831 |
|
| 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 |
0.862 |
|
| 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 |
0.839 |
|
| 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 |
0.826 |
|
| 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 |
0.838 |
|
| 2019 |
Lee GR, Won J, Heo L, Seok C. GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure. Nucleic Acids Research. PMID 31001635 DOI: 10.1093/nar/gkz288 |
0.85 |
|
| 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 |
0.623 |
|
| 2018 |
Bang I, Kim HR, Beaven AH, Kim J, Ko SB, Lee GR, Lee H, Im W, Seok C, Chung KY, Choi HJ. Biophysical and functional characterization of Norrin signaling through Frizzled4. Proceedings of the National Academy of Sciences of the United States of America. PMID 30104375 DOI: 10.1073/Pnas.1805901115 |
0.8 |
|
| 2018 |
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Seok C, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8 |
0.826 |
|
| 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 |
0.832 |
|
| 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 |
0.846 |
|
| 2017 |
Lee GR, Heo L, Seok C. Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment. Proteins. PMID 29044810 DOI: 10.1002/prot.25404 |
0.853 |
|
| 2017 |
Shao X, Kang H, Loveless T, Lee GR, Seok C, Weis WI, Choi HJ, Hardin J. Structural and functional characterization of the α-catenin·β-catenin binding interface in Caenorhabditis elegans reveals conserved requirements for cell-cell adhesion in metazoans. The Journal of Biological Chemistry. PMID 28842483 DOI: 10.1074/Jbc.M117.795567 |
0.702 |
|
| 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 |
0.826 |
|
| 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 |
0.864 |
|
| 2017 |
Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Human Mutation. PMID 28370845 DOI: 10.1002/Humu.23222 |
0.704 |
|
| 2017 |
Lee H, Seok C. Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock. Methods in Molecular Biology (Clifton, N.J.). 1561: 37-47. PMID 28236232 DOI: 10.1007/978-1-4939-6798-8_4 |
0.811 |
|
| 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 |
0.86 |
|
| 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 |
0.784 |
|
| 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 |
0.764 |
|
| 2016 |
Heo L, Lee H, Seok C. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking. Scientific Reports. 6: 32153. PMID 27535582 DOI: 10.1038/srep32153 |
0.862 |
|
| 2016 |
Lee GR, Seok C. Galaxy7TM: flexible GPCR-ligand docking by structure refinement. Nucleic Acids Research. PMID 27131365 DOI: 10.1093/nar/gkw360 |
0.766 |
|
| 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, ... ... Seok C, 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 |
0.844 |
|
| 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 |
0.855 |
|
| 2015 |
Ka D, Lee H, Jung YD, Kim K, Seok C, Suh N, Bae E. Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System. Structure (London, England : 1993). PMID 26671707 DOI: 10.1016/J.Str.2015.10.019 |
0.789 |
|
| 2015 |
Shin WH, Lee GR, Seok C. Evaluation of GalaxyDock based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies. Journal of Chemical Information and Modeling. PMID 26583962 DOI: 10.1021/acs.jcim.5b00309 |
0.831 |
|
| 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 |
0.845 |
|
| 2015 |
Lee GR, Heo L, Seok C. Effective protein model structure refinement by loop modeling and overall relaxation. Proteins. 293-301. PMID 26172288 DOI: 10.1002/prot.24858 |
0.857 |
|
| 2015 |
Lee S, Shin WH, Hong S, Kang H, Jung D, Yim UH, Shim WJ, Khim JS, Seok C, Giesy JP, Choi K. Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues. Chemosphere. 139: 23-29. PMID 26037956 DOI: 10.1016/J.Chemosphere.2015.05.033 |
0.697 |
|
| 2015 |
Lee KL, Singh AK, Heo L, Seok C, Roe JH. Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds. Molecular Microbiology. PMID 25998932 DOI: 10.1111/Mmi.13068 |
0.647 |
|
| 2015 |
Lee H, Heo L, Lee MS, Seok C. GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization. Nucleic Acids Research. PMID 25969449 DOI: 10.1093/nar/gkv495 |
0.843 |
|
| 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 |
0.859 |
|
| 2014 |
Heo L, Shin WH, Lee MS, Seok C. GalaxySite: ligand-binding-site prediction by using molecular docking. Nucleic Acids Research. 42: W210-4. PMID 24753427 DOI: 10.1093/nar/gku321 |
0.833 |
|
| 2014 |
Kim Y, Lee H, Heo L, Seok C, Choe J. Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif. Protein Science : a Publication of the Protein Society. 23: 906-14. PMID 24723367 DOI: 10.1002/Pro.2472 |
0.807 |
|
| 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, ... ... Seok C, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439 |
0.823 |
|
| 2013 |
Shin WH, Kim JK, Kim DS, Seok C. GalaxyDock2: protein-ligand docking using beta-complex and global optimization. Journal of Computational Chemistry. 34: 2647-56. PMID 24108416 DOI: 10.1002/jcc.23438 |
0.737 |
|
| 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, ... ... Seok C, 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 |
0.823 |
|
| 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 |
0.856 |
|
| 2013 |
Heo L, Cho YB, Lee MS, Roe JH, Seok C. Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors. Proteins. 81: 1644-52. PMID 23670838 DOI: 10.1002/Prot.24323 |
0.715 |
|
| 2013 |
Kim Y, Shin S, Kim T, Lee D, Seok C, Lee M. Switchable nanoporous sheets by the aqueous self-assembly of aromatic macrobicycles. Angewandte Chemie (International Ed. in English). 52: 6426-9. PMID 23649976 DOI: 10.1002/anie.201210373 |
0.591 |
|
| 2013 |
Lee D, Lee J, Seok C. What stabilizes close arginine pairing in proteins? Physical Chemistry Chemical Physics : Pccp. 15: 5844-53. PMID 23486862 DOI: 10.1039/c3cp00160a |
0.787 |
|
| 2013 |
Kim MS, Lee H, Heo L, Lim A, Seok C, Shin DH. New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies. Proteins. 81: 1499-508. PMID 23483653 DOI: 10.1002/prot.24275 |
0.806 |
|
| 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 |
0.857 |
|
| 2012 |
Shin WH, Seok C. GalaxyDock: protein-ligand docking with flexible protein side-chains. Journal of Chemical Information and Modeling. 52: 3225-32. PMID 23198780 DOI: 10.1021/ci300342z |
0.741 |
|
| 2012 |
Huang Z, Kang SK, Banno M, Yamaguchi T, Lee D, Seok C, Yashima E, Lee M. Pulsating tubules from noncovalent macrocycles. Science (New York, N.Y.). 337: 1521-6. PMID 22997334 DOI: 10.1126/SCIENCE.1224741 |
0.606 |
|
| 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 |
0.848 |
|
| 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 |
0.862 |
|
| 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 |
0.737 |
|
| 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, ... ... Seok C, 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 |
0.822 |
|
| 2011 |
Shin WH, Heo L, Lee J, Ko J, Seok C, Lee J. LigDockCSA: protein-ligand docking using conformational space annealing. Journal of Computational Chemistry. 32: 3226-32. PMID 21837636 DOI: 10.1002/jcc.21905 |
0.816 |
|
| 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 |
0.774 |
|
| 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 |
0.855 |
|
| 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 |
0.678 |
|
| 2011 |
Lee J, Lee J, Sasaki TN, Sasai M, Seok C, Lee J. De novo protein structure prediction by dynamic fragment assembly and conformational space annealing. Proteins. 79: 2403-17. PMID 21604307 DOI: 10.1002/prot.23059 |
0.729 |
|
| 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 |
0.842 |
|
| 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 |
0.826 |
|
| 2010 |
Lee J, Kim YG, Kim KK, Seok C. Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation. The Journal of Physical Chemistry. B. 114: 9872-81. PMID 20666528 DOI: 10.1021/jp103419t |
0.54 |
|
| 2010 |
Lee J, Kim JS, Seok C. Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study. The Journal of Physical Chemistry. B. 114: 7662-71. PMID 20469897 DOI: 10.1021/jp1017289 |
0.627 |
|
| 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 |
0.67 |
|
| 2008 |
Lee J, Seok C. A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect. Proteins. 70: 1074-83. PMID 18076034 DOI: 10.1002/prot.21844 |
0.686 |
|
| 2007 |
Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 3: 26-41. PMID 26627148 DOI: 10.1021/Ct0502864 |
0.608 |
|
| 2005 |
Coutsias EA, Seok C, Dill KA. Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. Journal of Computational Chemistry. 26: 1663-5. PMID 16175579 DOI: 10.1002/Jcc.20316 |
0.405 |
|
| 2005 |
Ho BK, Coutsias EA, Seok C, Dill KA. The flexibility in the proline ring couples to the protein backbone. Protein Science : a Publication of the Protein Society. 14: 1011-8. PMID 15772308 DOI: 10.1110/Ps.041156905 |
0.473 |
|
| 2004 |
Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. Journal of Computational Chemistry. 25: 1849-57. PMID 15376254 DOI: 10.1002/Jcc.20110 |
0.489 |
|
| 2004 |
Seok C, Freed KF, Szleifer I. Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces. The Journal of Chemical Physics. 120: 7174-82. PMID 15267625 DOI: 10.1063/1.1669372 |
0.344 |
|
| 2004 |
Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. Journal of Computational Chemistry. 25: 510-28. PMID 14735570 DOI: 10.1002/Jcc.10416 |
0.473 |
|
| 2003 |
Seok C, Rosen JB, Chodera JD, Dill KA. MOPED: method for optimizing physical energy parameters using decoys. Journal of Computational Chemistry. 24: 89-97. PMID 12483678 DOI: 10.1002/Jcc.10124 |
0.66 |
|
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