Derication of Class II Force Fields. I. Methology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules. - J. R. Maple; Ming-Jing Hwang; Thomas P. Stockfisch; Uri Dinur; Marvin Waldman; Carl S. Ewig; Arnold T. Hagler (J. Comput. Chem., 1994)

Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds. - J. R. Maple; Ming-Jing Hwang; Karl James Jalkanen; Thomas P. Stockfisch; Arnold T. Hagler (J. Comput. Chem., 1998)

Conformational analysis of three pyrophosphate model species: Diphosphate, methyl diphosphate, and triphosphate. - Ming-Jing Hwang; Pei-Ying Chu; Jye-Chan Chen; Ito Chao (J. Comput. Chem., 1999)

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds. - Carl S. Ewig; Rajiv Berry; Uri Dinur; Jörg-Rüdiger Hill; Ming-Jing Hwang; Haiying Li; Chris Liang; Jon Maple; Zhengwei Peng; Thomas P. Stockfisch; Thomas S. Thacher; Lisa Yan; et al. (J. Comput. Chem., 2001)

Protein structure comparison by probability-based matching of secondary structure elements. - Edward S. C. Shih; Ming-Jing Hwang (Bioinform., 2003)

Derivation and Analysis of Fragment Libraries of Protein Structures. - In-Yee Lee; Ta-tsen Soong; Jan-Ming Ho; Ming-Jing Hwang (BIBE, 2004)

The UniMarker (UM) method for synteny mapping of large genomes. - Ben-Yang Liao; Yu-Jung Chang; Jan-Ming Ho; Ming-Jing Hwang (Bioinform., 2004)

Classification of protein 3D folds by hidden Markov learning on sequences of structural alphabets. - Shiou-Ling Wang; Chung-Ming Chen; Ming-Jing Hwang (APBC, 2005)

A New Neural Network for B-Turn Prediction: the Effect of Site-Specific Amino Acid Preference. - Zhong-Ru Xie; Ming-Jing Hwang (APBC, 2006)

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)

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. - Edward S. C. Shih; Ruei-chi R. Gan; Ming-Jing Hwang (Nucleic Acids Res., 2006)

A network perspective on the topological importance of enzymes and their phylogenetic conservation. - Wei-Chung Liu; Wen-hsien Lin; Andrew J. Davis; Ferenc Jordán; Hsih-te Yang; Ming-Jing Hwang (BMC Bioinform., 2007)

Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. - Wen-hsien Lin; Wei-Chung Liu; Ming-Jing Hwang (BMC Syst. Biol., 2009)

An interaction-motif-based scoring function for protein-ligand docking. - Zhong-Ru Xie; Ming-Jing Hwang (BMC Bioinform., 2010)

Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles. - Zhong-Ru Xie; Ming-Jing Hwang (Bioinform., 2012)

A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits. - Austin W. T. Chiang; Ming-Jing Hwang (BMC Bioinform., 2013)

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites. - Zhong-Ru Xie; Chuan-Kun Liu; Fang-Chih Hsiao; Adam Yao; Ming-Jing Hwang (Nucleic Acids Res., 2013)

Hkera, a human transcriptome partitioner. - Austin W. T. Chiang; Grace Shaw; Ming-Jing Hwang (IWBBIO, 2014)

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters. - Austin W. T. Chiang; Wei-Chung Liu; Pep Charusanti; Ming-Jing Hwang (BMC Syst. Biol., 2014)

Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. - Austin W. T. Chiang; Walt Y. L. Wu; Ting Wang; Ming-Jing Hwang (PLoS Comput. Biol., 2017)