MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. - Darby Tien-Hao Chang; Yen-Jen Oyang; Jung-Hsin Lin (Nucleic Acids Res., 2005)

Protemot: prediction of protein binding sites with automatically extracted geometrical templates. - Darby Tien-Hao Chang; Yi-Zhong Weng; Jung-Hsin Lin; Ming-Jing Hwang; Yen-Jen Oyang (Nucleic Acids Res., 2006)

SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters. - Po-Hsien Lee; Kuei-Ling Kuo; Pei-Ying Chu; Eric Minwei Liu; Jung-Hsin Lin (Nucleic Acids Res., 2009)

On the Design of Optimization Algorithms for Prediction of Molecular Interactions. - Darby Tien-Hao Chang; Jung-Hsin Lin; Chih-Hung Hsieh; Yen-Jen Oyang (Int. J. Artif. Intell. Tools, 2010)

Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models. - Jui-Chih Wang; Jung-Hsin Lin; Chung-Ming Chen; Alex L. Perryman; Arthur J. Olson (J. Chem. Inf. Model., 2011)

AutoBind: automatic extraction of protein-ligand-binding affinity data from biological literature. - Darby Tien-Hao Chang; Chao-Hsuan Ke; Jung-Hsin Lin; Jung-Hsien Chiang (Bioinform., 2012)

idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. - Jui-Chih Wang; Pei-Ying Chu; Chung-Ming Chen; Jung-Hsin Lin (Nucleic Acids Res., 2012)

Prediction of Functional Types of Ligands for G Protein-Coupled Receptors with Dynamically Discriminable States Embedded in Low Dimension. - Yu-Hsuan Chen; Jung-Hsin Lin (IWBBIO (2), 2015)

A New Approach to the Discretization of Multidimensional Scaling. - Antonio Mucherino; Warley Gramacho; Jung-Hsin Lin; Carlile Lavor (FedCSIS, 2016)

An Efficient Exhaustive Search for the Discretizable Distance Geometry Problem with Interval Data. - Antonio Mucherino; Jung-Hsin Lin (FedCSIS, 2019)

A Coarse-Grained Representation for Discretizable Distance Geometry with Interval Data. - Antonio Mucherino; Jung-Hsin Lin; Douglas Soares Gonçalves (IWBBIO (1), 2019)

Delineating Protein-Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple-Walker Umbrella Sampling Simulations. - Dhananjay C. Joshi; Jung-Hsin Lin (J. Comput. Chem., 2019)

MD-jeep: a New Release for Discretizable Distance Geometry Problems with Interval Data. - Antonio Mucherino; Douglas Soares Gonçalves; Leo Liberti; Jung-Hsin Lin; Carlile Lavor; Nelson Maculan (FedCSIS, 2020)

Exploration of Conformations for an Intrinsically Disordered Protein. - Shu-Yu Huang; Chi-Fon Chang; Jung-Hsin Lin; Thérèse E. Malliavin (GSI (2), 2021)

The Coherent Multi-representation Problem for Protein Structure Determination. - Antonio Mucherino; Jung-Hsin Lin (DIS, 2023)

A generic method of pose generation in molecular docking via quadratic unconstrained binary optimization. - Pei-Kun Yang; Jung-Hsin Lin (FedCSIS (Position Papers), 2024)