Predicting protein-ligand binding site using support vector machine with protein properties

Identification of protein-ligand binding site is an important task in structure-based drug design and docking algorithms. In the past two decades, different approaches have been developed to predict the binding site, such as the geometric, energetic, and sequence-based methods. When scores are calculated from these methods, the algorithm for doing classification becomes very important and can affect the prediction results greatly. In this paper, the support vector machine (SVM) is used to cluster the pockets that are most likely to bind ligands with the attributes of geometric characteristics, interaction potential, offset from protein, conservation score, and properties surrounding the pockets. Our approach is compared to LIGSITE, LIGSITEcsc, SURFNET, Fpocket, PocketFinder, Q-SiteFinder, ConCavity, and MetaPocket on the data set LigASite and 198 drug-target protein complexes. The results show that our approach improves the success rate from 60 to 80 percent at AUC measure and from 61 to 66 percent at top 1 prediction. Our method also provides more comprehensive results than the others

Stanniocalcin-1 Reduces Tumor Size in Human Hepatocellular Carcinoma

Growing evidence has revealed high expression levels of stanniocalcin-1 (STC1) in different types of human cancers. Numerous experimental studies using cancer cell lines demonstrated the involvement of STC1 in inflammatory and apoptotic processes; however the role of STC1 in carcinogenesis remains elusive. Hepatocellular carcinoma (HCC) an exemplified model of inflammation-related cancer, represents a paradigm of studying the association between STC1 and tumor development. Therefore, we conducted a statistical analysis on the expression levels of STC1 using clinicopathological data from 216 HCC patients. We found that STC1 was upregulated in the tumor tissues and its expression levels was positively correlated with the levels of interleukin (IL)-6 and IL-8. Intriguingly tumors with greater expression levels of STC1 (tumor/normal >= 2) were significantly smaller than the lower level (tumor/normal<2) samples (p = 0.008). A pharmacological approach was implemented to reveal the functional correlation between STC1 and the ILs in the HCC cell-lines. IL-6 and IL-8 treatment of Hep3B cells induced STC1 expression. Lentiviral-based STC1 over-expression in Hep3B and MHCC-97L cells however showed inhibitory action on the pro-migratory effects of IL-6 and IL-8 and reduced size of tumor spheroids. The inhibitory effect of STC1 on tumor growth was confirmed in vivo using the stable STC1-overexpressing 97L cells on a mouse xenograft model. Genetic analysis of the xenografts derived from the STC1-overexpressing 97L cells, showed upregulation of the pro-apoptotic genes interleukin-12 and NOD-like receptor family, pyrin domain-containing 3. Collectively, the anti-inflammatory and pro-apoptotic functions of STC1 were suggested to relate its inhibitory effect on the growth of HCC cells. This study supports the notion that STC1 may be a potential therapeutic target for inflammatory tumors in HCC patients.published_or_final_versio

Did Obamacare encourage business to hire more people? - an analysis of Mitt Romney and Barack Obama’s use of rhetorical questions in the 2012 US presidential election campaign

2013-2014 > Academic research: refereed > Refereed conference paperOther Versio

Did Obamacare create new jobs? - an analysis of Mitt Romney’s use of rhetorical questions in the 2012 US presidential election campaign

2013-2014 > Academic research: refereed > Refereed conference paperOther Versio

An analysis of the use of rhetorical questions in the 2012 Legislative Council election debates in Hong Kong

2013-2014 > Academic research: refereed > Refereed conference paperOther Versio

From classifier to stance marker : on the diachronic development of Cantonese go³

2011-2012 > Academic research: refereed > Refereed conference paperOther Versio

On the the grammaticalization of stative verbs into continuative markers : the case of Malay asyik ‘desire’ and Cantonese gwaazyu ‘keep thinking about'

The conference was hosted by the Department of Linguistics, Faculty of Arts, Chulalongkorn University, the ASEAN Studies Center, the Institute of Asian Studies, Chulalongkorn University, and the National Institute of Japanese Language and Linguistics (NINJAL), Japan.2012-2013 > Academic research: refereed > Refereed conference paperOther Versio

Valence-changing phenomena and stance marking in Chinese : on the development of 共 in Classical Chinese and Southern Min

2013-2014 > Academic research: refereed > Refereed conference paperOther Versio

A diachronic study of epistemic kongpa in Mandarin discourse

The conference was hosted by Graduate Institute of Linguistics, Department of Psychology, Neurobiology and Cognitive Science Center at National Taiwan University, and Linguistic Society of Taiwan2011-2012 > Academic research: refereed > Refereed conference paperOther Versio

“I am sure but I hedge” : fear expression kongpa as a rhetorical interactive strategy in Mandarin conversation

2012-2013 > Academic research: refereed > Refereed conference paperOther Versio