MOPED: Method for optimizing physical energy parameters using decoys. - Chaok Seok; J. Ben Rosen; John D. Chodera; Ken A. Dill (J. Comput. Chem., 2003)

Using quaternions to calculate RMSD. - Evangelos A. Coutsias; Chaok Seok; Ken A. Dill (J. Comput. Chem., 2004)

A kinematic view of loop closure. - Evangelos A. Coutsias; Chaok Seok; Matthew P. Jacobson; Ken A. Dill (J. Comput. Chem., 2004)

Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. - Evangelos A. Coutsias; Chaok Seok; Ken A. Dill (J. Comput. Chem., 2005)

LigDockCSA: Protein-ligand docking using conformational space annealing. - Woong-Hee Shin; Lim Heo; Juyong Lee; Junsu Ko; Chaok Seok; Jooyoung Lee 002 (J. Comput. Chem., 2011)

The FALC-Loop web server for protein loop modeling. - Junsu Ko; Dongseon Lee; Hahnbeom Park; Evangelos A. Coutsias; Julian Lee; Chaok Seok (Nucleic Acids Res., 2011)

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. - Junsu Ko; Hahnbeom Park; Chaok Seok (BMC Bioinform., 2012)

GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains. - Woong-Hee Shin; Chaok Seok (J. Chem. Inf. Model., 2012)

GalaxyWEB server for protein structure prediction and refinement. - Junsu Ko; Hahnbeom Park; Lim Heo; Chaok Seok (Nucleic Acids Res., 2012)

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity. - Hasup Lee 002; Hahnbeom Park; Junsu Ko; Chaok Seok (Bioinform., 2013)

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization. - Woong-Hee Shin; Jae-Kwan Kim 001; Deok-Soo Kim; Chaok Seok (J. Comput. Chem., 2013)

GalaxyRefine: protein structure refinement driven by side-chain repacking. - Lim Heo; Hahnbeom Park; Chaok Seok (Nucleic Acids Res., 2013)

GalaxySite: ligand-binding-site prediction by using molecular docking. - Lim Heo; Woong-Hee Shin; Myeong Sup Lee; Chaok Seok (Nucleic Acids Res., 2014)

GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization. - Hasup Lee 002; Lim Heo; Myeong Sup Lee; Chaok Seok (Nucleic Acids Res., 2015)

Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies. - Woong-Hee Shin; Gyu Rie Lee; Chaok Seok (J. Chem. Inf. Model., 2016)

Galaxy7TM: flexible GPCR-ligand docking by structure refinement. - Gyu Rie Lee; Chaok Seok (Nucleic Acids Res., 2016)

GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking. - Minkyung Baek; Woong-Hee Shin; Hwan Won Chung; Chaok Seok (J. Comput. Aided Mol. Des., 2017)

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. - Juyong Lee; Florentina Tofoleanu; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Ana Damjanovic; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

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. - Florentina Tofoleanu; Juyong Lee; Frank C. Pickard IV; Gerhard König; Jing Huang 004; Minkyung Baek; Chaok Seok; Bernard R. Brooks (J. Comput. Aided Mol. Des., 2017)

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure. - Minkyung Baek; Taeyong Park 002; Lim Heo; Chiwook Park; Chaok Seok (Nucleic Acids Res., 2017)

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors. - Jonghun Won; Gyu Rie Lee; Hahnbeom Park; Chaok Seok (J. Chem. Inf. Model., 2018)

GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters. - Taeyong Park 002; Minkyung Baek; Hasup Lee 002; Chaok Seok (J. Comput. Chem., 2019)

GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility. - Jinsol Yang; Minkyung Baek; Chaok Seok (J. Comput. Chem., 2019)

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure. - Gyu Rie Lee; Jonghun Won; Lim Heo; Chaok Seok (Nucleic Acids Res., 2019)

Prediction of Molecular Electronic Transitions Using Random Forests. - Beomchang Kang; Chaok Seok; Juyong Lee (J. Chem. Inf. Model., 2020)

GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds. - Jinsol Yang; Sohee Kwon; Sang-Hun Bae; Kyoung Mii Park; Changsik Yoon; Ji-Hyun Lee; Chaok Seok (J. Chem. Inf. Model., 2020)

GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential. - Lim Heo; Sangwoo Park; Chaok Seok (J. Chem. Inf. Model., 2021)

GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking. - Taeyong Park 002; Jonghun Won; Minkyung Baek; Chaok Seok (Nucleic Acids Res., 2021)

GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network. - Sangwoo Park; Chaok Seok (J. Chem. Inf. Model., 2022)

Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design. - Seho Lee; Chaok Seok; Hahnbeom Park (J. Comput. Chem., 2023)

GalaxyDock2-HEME: Protein-ligand docking for heme proteins. - Changsoo Lee; Jinsol Yang; Sohee Kwon; Chaok Seok (J. Comput. Chem., 2023)

HProteome-BSite: predicted binding sites and ligands in human 3D proteome. - Jiho Sim; Sohee Kwon; Chaok Seok (Nucleic Acids Res., 2023)

Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. - Hyeonuk Woo; Yubeen Kim; Chaok Seok (PLoS Comput. Biol., 2024)

CSearch: chemical space search via virtual synthesis and global optimization. - Hakjean Kim; Seongok Ryu; Nuri Jung; Jinsol Yang; Chaok Seok (J. Cheminformatics, 2024)

Deep learning molecular interaction motifs from receptor structures alone. - Seeun Kim; Simaek Oh; Hyeonuk Woo; Jiho Sim; Chaok Seok; Hahnbeom Park (J. Cheminformatics, 2025)