G-TBLD
A computational tool to design small molecule ligands using chemical fragment templates
LigFrag
Computational tool to dissect ligands into chemical fragments
CMCS-BSP
A computational tool to predict small-molecule and protein binding sites
Ligand binding site detection by local structure alignment and its performance complementarity
Hui Sun Lee and Wonpil Im
J. Chem. Inf. Model. 2013, 53: 2462-2470
G-LoSA
A computational tool to identify the best structural alignment and provide the normalized measurement of structural similarity between different protein local structures
G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.
Hui Sun Lee and Wonpil Im.
In Methods in Molecular Biology: Function Prediction, 2017, Daisuke Kihara Ed.
G-LoSA: An Efficient Computational Tool for Local Structure-Centric Biological Studies and Drug Design.
Hui Sun Lee and Wonpil Im.
Protein Sci. 2016, 25: 865-876
Ligand binding site detection by local structure alignment and its performance complementarity
Hui Sun Lee and Wonpil Im
J. Chem. Inf. Model. 2013, 53: 2462-2470
Identification of ligand templates using local structure alignment for structure-based drug design
Hui Sun Lee and Wonpil Im
J. Chem. Inf. Model. 2012, 52: 2784-2795
GS-Align
A computational tool to identify the best structural alignment and provide the normalized measurement of structural similarity between different glycan structures
GS-align for Glycan Structure Alignment and Similarity Measurement
Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, and Wonpil Im
Bioinformatics (in press)
CHARMM-GUI Micelle Builder
CHARMM input file generator for molecular dynamics simulation of a protein/micelle complex
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda and Wonpil Im
J. Chem. Inf. Model. 2013, 53: 2171-2180
CHARMM-GUI Ligand Binder
CHARMM input file generator to calculate protein/ligand absolute binding free energy
CHARMM-GUI ligand binder for absolute binding free energy calculations and its application
Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, and Wonpil Im
J. Chem. Inf. Model. 2013, 53: 267-277
BSP-SLIM
High-speed blind ligand docking program particularly applicable to predicted protein models
BSP-SLIM: a blind low-resolution ligand-protein docking approach using theoretically predicted protein structures
Hui Sun Lee and Yang Zhang
Proteins 2012, 80: 93-110
SLIM
High-speed receptor-centric virtual screening program using shape and chemical feature complementarity between compounds and binding pocket
Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket
Hui Sun Lee, Cheol Soon Lee, Jeong Sook Kim, Dong Hou Kim, Han Choe
J. Chem. Inf. Model. 2009, 49: 2419-2428
QHELIX
Software for the improved measurement of inter-helical angles in proteins
QHELIX: a computational tool for the improved measurement of inter-helical angles in proteins
Hui Sun Lee, Jiwon Choi, Sukjoon Yoon
Protein J. 2007 26: 556-561
CAPSID
Software to design siRNAs using highly conserved patterns in multiple sequences
A novel program to design siRNAs simultaneously effective to highly variable virus genomes
Hui Sun Lee, Jeonghyun Ahn, Eun Jung Jun, Sanghwa Yang, Chul Hyun Joo, Yoo Kyum Kim, Heuiran Lee
Biochem. Biophys. Res. Commun. 2009, 384: 431-435
SELF-ASSEMBLER
Molecular dynamics simulation software based on parallel computation
Contributions of 3´-overhang to the dissociation of small interfering RNAs from the PAZ domain: molecular dynamics simulation study
Hui Sun Lee, Soo Nam Lee, Chul Hyun Joo, Heuiran Lee, Han Saem Lee, Seung Yong Yoon, Yoo Kyum Kim, Han Choe
J. Mol. Graph. Model. 2007 25:784-793
Targeted molecular dynamics simulation studies of calcium binding and conformational change in the C-terminal half of gelsolin
Hui Sun Lee, Robert Charles Robinson, Chul Hyun Joo, Heuiran Lee, Yoo Kyum Kim, Han Choe
Biochem. Biophys. Res. Commun. 2006 342:702-709