Correlated Mutation Analysis
Residue-Residue Coevolution Network (RRCN)
B-C. Lee, K. Park, D. Kim, “Analysis of the residue-residue coevolution network and the functionally important residues in proteins”, Proteins, 72(3):863-872 (2008)
Reduction of normalised coevolutionary pattern similarity (NCPS) scores: CMc and aMIc method
Inkyung Jung and Dongsup Kim. (2010) The effect of histone modifications on gene regulation differs according to biological function, in submissionImpoHis
Reference
Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida, and Dongsup Kim. (2010) PostMod: Sequence-based prediction of phosphorylation sites by considering indirect relationships, BMC bioinformatics PostMod
Reference
Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe
Supplementary page
Kim DU, Hayles J, Kim D, Wood V, Park HO, Won M, Yoo HS, Duhig T, Nam M, Palmer G, Han S, Jeffery L, Baek ST, Lee H, Shim YS, Lee M, Kim L, Heo KS, Noh EJ, Lee AR, Jang YJ, Chung KS, Choi SJ, Park JY, Park Y, Kim HM, Park SK, Park HJ, Kang EJ, Kim HB, Kang HS, Park HM, Kim K, Song K, Song KB, Nurse P, Hoe KL., “Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe”, Nat Biotech, 28(6):617-23 (2010)
Reduction of normalised coevolutionary pattern similarity (NCPS) scores: CMc and aMIc method
LibBP: Library of Binding Protein
Reference
Seungpyo Hong, and Dongsup Kim. "Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds." Bioinformatics (2016)
KRDS: Kinase Resistance Docking System
Reference
A, and Dongsup Kim. "Kinase Resistance Docking System" in submission
RF-QSAR: Random Forest based target fishing server
Reference
Kyoungyeul Lee, Minho Lee, and Dongsup Kim. "Utilizing Random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server ", BMC bioinformatics, accepted
3DIV: A 3D-genome Interaction Viewer and database
Reference
Dongchan Yang, Insu Jang, Jinhyuk Choi, Min-Seo Kim, Andrew J. Lee, Hyunwoong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, and Byungwook Lee. "3DIV: A 3D-genome Interaction Viewer and database", Nucleic Acids Research
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction
Reference
Han Y, Kim D. Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction. BMC bioinformatics. 2017 Dec;18(1):585.