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)

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

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)

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

PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. - Woong-Hee Shin; Charles Christoffer; Ji-Bo Wang; Daisuke Kihara (J. Chem. Inf. Model., 2016)

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)

Combined Approach of Patch-Surfer and PL-PatchSurfer for Protein-Ligand Binding Prediction in CSAR 2013 and 2014. - Xiaolei Zhu 001; Woong-Hee Shin; Hyungrae Kim; Daisuke Kihara (J. Chem. Inf. Model., 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)

Modeling the assembly order of multimeric heteroprotein complexes. - Lenna X. Peterson; Yoichiro Togawa; Juan Esquivel-Rodríguez; Genki Terashi; Charles Christoffer; Amitava Roy; Woong-Hee Shin; Daisuke Kihara (PLoS Comput. Biol., 2018)

Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0. - Woong-Hee Shin; Daisuke Kihara (J. Comput. Aided Mol. Des., 2019)

Three-dimensional Krawtchouk descriptors for protein local surface shape comparison. - Atilla Sit; Woong-Hee Shin; Daisuke Kihara (Pattern Recognit., 2019)

Study of the Variability of the Native Protein Structure. - Xusi Han; Woong-Hee Shin; Charles Christoffer; Genki Terashi; Lyman Monroe; Daisuke Kihara (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

SHREC 2021: Surface-based Protein Domains Retrieval. - Florent Langenfeld; Tunde Aderinwale; Charles Christoffer; Woong-Hee Shin; Genki Terashi; Xiao Wang 004; Daisuke Kihara; Halim Benhabiles; Karim Hammoudi; Adnane Cabani; Féryal Windal; Mahmoud Melkemi; et al. (3DOR, 2021)

SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties. - Andrea Raffo; Ulderico Fugacci; Silvia Biasotti; Walter Rocchia; Yonghuai Liu; Ekpo Otu; Reyer Zwiggelaar; David Hunter; Evangelia I. Zacharaki; Eleftheria Psatha; Dimitrios Laskos; Gerasimos Arvanitis; et al. (Comput. Graph., 2021)

Accurate prediction of protein-ligand interactions by combining physical energy functions and graph-neural networks. - Yiyu Hong; Junsu Ha; Jaemin Sim; Chae Jo Lim; Kwang-Seok Oh; Ramakrishnan Chandrasekaran; Bomin Kim; Jieun Choi; Junsu Ko; Woong-Hee Shin; Juyong Lee (J. Cheminformatics, 2024)