In silico drug design by integrated technology

Galux drug design technology is based on fundamental physical principles, so it covers all areas of protein drug, peptide drug, and small-molecule drug design.

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Protein drug design

Galux has specialized softwares to predict protein-protein interactions, which is directly applied to designing new protein drugs effectively. Galux protein-protein interaction prediction method showed outstanding performances in CAPRI international competitions.

Peptide drug design

Peptide and peptidomimetic drugs can be rationally designed based on Galux protein-peptide interaction prediction technology. Galux protein-peptide interaction prediction method showed outstanding performances in CAPRI international competitions.

Small-molecule drug design

Galux small-molecule drug design software is based on prediction of atomistic interactions of protein and small molecules by physics-inspired deep learning methods. Galux protein-ligand interaction showed outstanding performances in international competitions such as GPCRDock and CSAR.

 

Papers related to Galux technology

Protein structure prediction

  • G. R. Lee, J. Won, L. Heo, and C. Seok, GalaxyRefine2: Simultaneous refinement of inaccurate local regions and overall protein structure, Nucleic Acids Res. 47 (W1), W451-W455 (2019).

  • G. R. Lee, L. Heo, and C. Seok, Effective protein model structure refinement by loop modeling and overall relaxation, Proteins: Structure, Function, and Bioinformatics, 84 (S1), 293-301 (2016). 

  • H. Park, G. R. Lee, L. Heo, and C. Seok, Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments, PLoS ONE 9 (11): e113811 (2014).

  • J. Ko, H. Park, and C. Seok, GalaxyTBM: template-based modeling by building a reliable core

  • and refining unreliable local regions, BMC Bioinformatics, 13, 198 (2012).

  • J. Ko, H. Park, L. Heo, and C. Seok, GalaxyWEB server for protein structure prediction and refinement, Nucleic Acids Res. 40 (W1), W294-W297 (2012).

  • H. Park and C. Seok, Refinement of unreliable local regions in template-based protein models, Proteins: Structure, Function, and Bioinformatics, 80 (8), 1974-1986 (2012).

  • L. Heo, H. Park, and C. Seok, GalaxyRefine: Protein structure refinement driven by side-chain repacking, Nucleic Acids Res. 41 (W1), W384-W388 (2013).

  • J. Ko, D. Lee, H. Park, E. A. Coutsias, J. Lee, and C. Seok, The FALC-Loop web server for protein loop modeling, Nucleic Acids Res. 39, W210-W214 (2011).

  • J. Lee, D. Lee, H. Park, E. A. Coutsias, and C. Seok, Protein loop modeling by using fragment assembly and analytical loop closure, Proteins: Structure, Function, and Bioinformatics, 78, 3428-3436 (2010).

Prediction of protein-protein interactions

  • T. Park, H. Woo, M. Baek, J. Yang, and C. Seok, Structure Prediction of Biological Assemblies using GALAXY in CAPRI Rounds 38-45, Proteins: Structure, Function, and Bioinformatics, 88 (8), 1009-1017 (2020).

  • M. Baek, T. Park, H. Woo, and C. Seok, Prediction of Protein Oligomer Structures using GALAXY in CASP13, Proteins: Structure, Function, and Bioinformatics, 87 (12), 1233-1240 (2019).

  • T. Park, M. Baek, H. Lee, and C. Seok, GalaxyTongDock: symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters, J. Comput. Chem. 40 (27) 2413-2417 (2019). [cover article]

  • L. Heo, H. Lee and C. Seok, GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking, Sci. Rep., 6, 32153 (2016).

  • H. Lee, M. Baek, G. R. Lee, S. Park, and C. Seok, Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30, Proteins: Structure, Function, and Bioinformatics, 85 (3), 399-407 (2017). (back cover article)

  • M. Baek, T. Park, L. Heo, C. Park, and C. Seok, GalaxyHomomer: A web server for protein homo-oligomer structure prediction from a monomer sequence or structure, Nucleic Acids Res. 45 (W1), W320-W324 (2017). 

  • 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).

  • H. Lee, H. Park, J. Ko, and C. Seok, GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity, Bioinformatics, 29 (8), 1078-1080 (2013).

Prediction of protein-ligand interactions

  • J. Yang, S. Kwon, S.-H. Bae, K. M. Park, C. Yoon, J.-H. Lee, and C. Seok, GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds, J. Chem. Inf. Model, 60 (6), 3246-3254 (2020). 

  • J. Yang, M. Baek, and C. Seok, GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility, J. Comput. Chem. 40 (31), 2739-2748 (2019).

  • M. Baek, W. -H. Shin, H. W. Chung, and C. Seok, GalaxyDock BP2 Score: A Hybrid Scoring Function for Accurate Protein-Ligand Docking, J. Comput. Aid. Mol. Design. 31 (7), 653-666 (2017). 

  • G. R. Lee and C. Seok, Galaxy7TM: Flexible GPCR-ligand docking by structure refinement, Nucleic Acids Res. 44 (W1), W502-506 (2016). 

  • W. -H. Shin, G. R. Lee, and C. Seok, Evaluation of GalaxyDock based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies, J. Chem. Inf. Model, 56 (6), 988-995 (2016).

  • H. Lee, L. Heo, M. S. Lee, and C. Seok, GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization, Nucleic Acids Res. 43 (W1), W431-W435 (2015).

  • L. Heo, W. -H. Shin, M. S. Lee, and C. Seok, GalaxySite: Ligand-binding site prediction by using molecular docking, Nucleic Acids Res. 42 (W1), W210-W214 (2014). 

  • W. -H. Shin, J. -K. Kim, D. -S. Kim, and C. Seok, GalaxyDock2: Protein-ligand docking using beta-complex and global optimization, J. Comput. Chem. 34 (30), 2647-2656 (2013). 

  • W. -H. Shin and C. Seok, GalaxyDock: Protein-ligand docking with flexible protein side-chains, J. Chem. Inf. Model, 52 (12), 3225-3232 (2012).