Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Taiwan
Welcome to our laboratory, we are interested in the following topics:
Cancer related single amino acid variation

 

Cancer-related single amino acid variation:

 

  • Liu JJ, Yu CS, Wu HW, Chang YJ, Lin CP and Lu CH*. The structurebased cancerrelated single amino acid variation prediction. Scientific Reports (2021), 11, Article number: 13599.
  • Lin YF, Liu JJ, Chang YJ, Yu CS, Yi W, Lane HY and Lu CH*. Predicting anticancer drug resistance mediated by mutations. Pharmaceuticals (2022), 15(2), 136.

 
 
Metal ion-binding sites detection and modeling

 

Metal ion-binding sites detection and modeling:

 

  • Lu CH, Chen CC, Yu CS, Liu YY, Liu JJ, Wei ST, Lin YF*. MIB2: Metal ion-binding site prediction and modeling server. Bioinformatics (2022), btac534.
  • Lin YF, Cheng CW, Shih CS, Hwang JK, Yu CS and Lu CH*. MIB: Metal Ion-Binding site prediction and docking server. Journal of Chemical Information and Modeling (2016), 56 (12), pp 22872291
  • Lu CH*, Lin YF, Lin JJ, Yu CS. Prediction of Metal Ion-Binding Sites in Proteins Using the Fragment Transformation Method. PLoS One (2012), 7(6):e39252

 
 
Computer-aided drug design

 

Computer-aided drug design:

 

  • Chang YJ, Nguyen U, Liu JJ, Li SR, Chao ST, Lai HC, Lin YF, Hsu KC, Lu CH* and Lin CW*. Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV. Antiviral Research (2023), 216: 105653.
  • Lu CH, Chang HT, Hsu LF, Lee MH, Cheng J, Wu DC and Lin WY*. In Silico and In Vitro Screening of Serine Racemase Agonist and In Vivo Efficacy on Alzheimers Disease Drosophila melanogaster. Pharmaceuticals (2023), 16(2): 280.
  • Lu CH, Chung WM, Tsai CH, Cheng JC, Hsu KC and Tzeng HE*. In vitro characterization of a small molecule PD-1 inhibitor that targets the PD-l/PD-L1 interaction. Scientific Reports (2022), 12, Article number: 303.
  • Chang YJ, Yeh CY, Cheng JC, Huang YQ, Hsu KC, Lin YF and Lu CH*. Potent sialic acid inhibitors that target influenza A virus hemagglutinin. Scientific Reports (2021), 11, Article number: 8637.

 
 
Localization prediction and functional annotation

 

Localization prediction and functional annotation:

 

  • Yu CS, Cheng CW, Chang KC, Su WC, Huang SW, Hwang JK and Lu CH*. CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation. PLoS One (2014), 9(6):e99368
  • Yu CS, Chen YC, Lu CH, Hwang JK*. Prediction of protein subcellular localization. Proteins: Sturcture, Function and Bioinformatics (2006), 64: 643-51

 
 
Systems biology and machine learning

 

Systems biology and machine learning:

 

  • Lu CH, Wei ST, Liu JJ, Chang YJ, Lin YF, Yu CS and Chang LY*. Recognition of a Novel Gene Signature for Human Glioblastoma. International Journal of Molecular Sciences (2022), 23(8):4157.
  • Yu CS* and Lu CH. Identification of Antifreeze Proteins and Their Functional Residues by Support Vector Machine and Genetic Algorithms based on n-Peptide Compositions. PLoS One (2011), 6(5):e20445
  • Lu CH, Chen YC, Yu CS, Hwang JK*. Predicting disulfide connectivity patterns. Proteins: Structure, Function and Bioinformatics (2007), 67: 262-70

 
 
Protein dynamics:

 

Protein dynamics:

 

  • Lu CH, Huang SW, Lai YL, Lin CP, Shih CH, Huang CC, Hsu WL and Hwang JK*. On the relationship between the protein structure and protein dynamics. Proteins: Structure, Function and Bioinformatics (2008), 72: 625-34
  • Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, Huang CC and Hwang JK*. Deriving protein dynamical properties from weighted protein contact number. Proteins: Structure, Function and Bioinformatics (2008), 72: 929-35