Automated assignment of backbone NMR peaks using constrained bipartite matching. - Ying Xu 001; Dong Xu 002; Dongsup Kim; Victor Olman; Jane Razumovskaya; Tao Jiang 001 (Comput. Sci. Eng., 2002)

Protein Threading by Linear Programming. - Jinbo Xu; Ming Li 001; Guo-Hui Lin; Dongsup Kim; Ying Xu 001 (Pacific Symposium on Biocomputing, 2003)

A computational pipeline for protein structure prediction and analysis at genome scale. - Manesh J. Shah; Sergei Passovets; Dongsup Kim; Kyle Ellrott; Li Wang 008; Inna Vokler; Philip F. LoCascio; Dong Xu 002; Ying Xu 001 (Bioinform., 2003)

Raptor: Optimal Protein Threading by Linear Programming. - Jinbo Xu; Ming Li 001; Dongsup Kim; Ying Xu 001 (J. Bioinform. Comput. Biol., 2003)

Fold recognition by combining profile-profile alignment and support vector machine. - Sangjo Han; Byung-chul Lee; Seung Taek Yu; Chan-seok Jeong; Soyoung Lee; Dongsup Kim (Bioinform., 2005)

AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs. - Sangjo Han; Dongsup Kim (BMC Bioinform., 2006)

Inference of Gene Regulatory Networks Using Time Sliding Comparison and Transcriptional Lagging Time from Time Series Gene Expression Profiles. - Sheehyun Kim; Dongsup Kim (BIBE, 2007)

Predicting and improving the protein sequence alignment quality by support vector regression. - Minho Lee 002; Chan-seok Jeong; Dongsup Kim (BMC Bioinform., 2007)

Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. - Inkyung Jung; Jaehyung Lee 001; Soo-Young Lee; Dongsup Kim (BMC Bioinform., 2008)

Inference of Protein Complex Activities from Chemical-Genetic Profile and Its Applications: Predicting Drug-Target Pathways. - Sangjo Han; Dongsup Kim (PLoS Comput. Biol., 2008)

SIMPRO: simple protein homology detection method by using indirect signals. - Inkyung Jung; Dongsup Kim (Bioinform., 2009)

A new method for revealing correlated mutations under the structural and functional constraints in proteins. - Byung-chul Lee; Dongsup Kim (Bioinform., 2009)

Linear predictive coding representation of correlated mutation for protein sequence alignment. - Chan-seok Jeong; Dongsup Kim (BMC Bioinform., 2010)

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. - Inkyung Jung; Akihisa Matsuyama; Minoru Yoshida; Dongsup Kim (BMC Bioinform., 2010)

Modeling allosteric signal propagation using protein structure networks. - Keunwan Park; Dongsup Kim (BMC Bioinform., 2011)

Drug-drug relationship based on target information: application to drug target identification. - Keunwan Park; Dongsup Kim (BMC Syst. Biol., 2011)

Coevolved Residues and the Functional Association for Intrinsically Disordered Proteins. - Chan-seok Jeong; Dongsup Kim (Pacific Symposium on Biocomputing, 2012)

Large-scale reverse docking profiles and their applications. - Minho Lee 002; Dongsup Kim (BMC Bioinform., 2012)

A checkpoints capturing timing-robust Boolean model of the budding yeast cell cycle regulatory network. - Changki Hong; Minho Lee 002; Dongsup Kim; Dong San Kim; Kwang-Hyun Cho; Insik Shin (BMC Syst. Biol., 2012)

FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action. - Minho Lee 002; Sangjo Han; Hyeshik Chang; Youn-Sig Kwak; David M. Weller; Dongsup Kim (BMC Genom., 2013)

Interaction network among functional drug groups. - Minho Lee 002; Keunwan Park; Dongsup Kim (BMC Syst. Biol., 2013)

Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds. - Seungpyo Hong; Dongsup Kim (Bioinform., 2016)

Structure-based Markov random field model for representing evolutionary constraints on functional sites. - Chan-seok Jeong; Dongsup Kim (BMC Bioinform., 2016)

Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction. - Youngmahn Han; Dongsup Kim (BMC Bioinform., 2017)

Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server. - Kyoungyeul Lee; Minho Lee 002; Dongsup Kim (BMC Bioinform., 2017)

KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking. - Aeri Lee; Seungpyo Hong; Dongsup Kim (J. Cheminformatics, 2018)

3DIV: A 3D-genome Interaction Viewer and database. - Dongchan Yang; Insu Jang; Jinhyuk Choi; Minseo Kim; Andrew J. Lee; Hyun-Woong Kim; Junghyun Eom; Dongsup Kim; Inkyung Jung; Byungwook Lee (Nucleic Acids Res., 2018)

FP2VEC: a new molecular featurizer for learning molecular properties. - Woosung Jeon; Dongsup Kim (Bioinform., 2019)

Prediction of mutation effects using a deep temporal convolutional network. - Ha Young Kim; Dongsup Kim (Bioinform., 2020)

CRDS: Consensus Reverse Docking System for target fishing. - Aeri Lee; Dongsup Kim (Bioinform., 2020)

DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator. - Dongchan Yang; Taesu Chung; Dongsup Kim (Bioinform., 2022)

AbFlex: designing antibody complementarity determining regions with flexible CDR definition. - Woosung Jeon; Dongsup Kim (Bioinform., 2024)