Choong Yee Siew
Name
Choong Yee Siew
Current Position
Associate Professor
yeesiew@usm.my
Office Telephone
+604-6534837
Qualifications
PhD, Universiti Sains Malaysia, 2008
Research Interests
Molecular modelling, Computer aided antibody design and optimization, Protein structure prediction; Molecular docking and dynamics simulation
Research Overview 1
Molecular modelling in biological research
Powerful techniques in molecular biology, x-ray crystallography and nuclear magnetic resonance spectroscopy have led to high resolution of biomolecules’ three dimensional structures. However, due to limitation of the experimental methods, molecular modelling has been applied to elucidate biomolecules’ structures. In addition, advances made in computational resources have also enabled the dynamics and the interactions of biomolecules with other molecules to be elucidated. The structural analysis could thus inform structure-function relationship as well as the modelling of biological system.
Research Overview 2
Computer-aided antibody design
Computer aided antibody design or de novo antibody design has been used to facilitate antibody discovery for diagnostics, vaccine developments or next-generation protein therapeutics due to the time and cost require by experimental approaches. The antibodies can be designed or optimized for higher affinity where the interactions with the target can be modelled at molecular level. Successful examples have been reported in the modelling at e.g. CDRs for affinity improvement and Fc effector region for modulating immune cell activity. Given that a slight error in each step could be amplified in the subsequent steps, each step in antibody design need to be studied attentively.
Selected Publications
1. Chin CF, Lai JY, Choong YS, Anthony AA, Ismail A, Lim TS. Delineation of B-cell Epitopes of Salmonella enterica serovar Typhi Hemolysin E: Potential antibody therapeutic target. Sci Rep. 2017 May 19;7(1):2176. doi: 10.1038/s41598-017-01987-8. PMID: 28526816.
2. Khor BY, Tye GJ, Lim TS, Choong YS.General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model. 2015 Sep 4;12:15. doi: 10.1186/s12976-015-0014-1. Review. PMID: 26338054.
3. Lee YV, Wahab HA, Choong YS. Potential inhibitors for isocitrate lyase of Mycobacterium tuberculosis and non-M. tuberculosis: a summary. Biomed Res Int. 2015;2015:895453. doi: 10.1155/2015/895453. Epub 2015 Jan 8. Review. PMID: 25649791.
4. Leong SW, Lim TS, Tye GJ, Ismail A, Aziah I, Choong YS. Assembly and stability of Salmonella enterica ser. Typhi TolC protein in POPE and DMPE. J Biol Phys. 2014 Sep;40(4):387-400. doi: 10.1007/s10867-014-9357-9. Epub 2014 Jul 11. PMID: 25011632.
5. Khor BY, Tye GJ, Lim TS, Noordin R, Choong YS.The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. Int J Mol Sci. 2014 Jun 19;15(6):11082-99. doi: 10.3390/ijms150611082. PMID: 24950179.
6. Choong YS, Tye GJ, Lim TS. Minireview: applied structural bioinformatics in proteomics. Protein J. 2013 Oct;32(7):505-11. doi: 10.1007/s10930-013-9514-1. Review. PMID: 24096348.
7. Tommy YB, Lim TS, Noordin R, Saadatnia G, Choong YS. Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii. BMC Struct Biol. 2012 Nov 27;12:30. doi: 10.1186/1472-6807-12-30. PMID: 23181504.
8. Yung-Hung RL, Ismail A, Lim TS, Choong YS. A 35 kDa antigenic protein from Shigella flexneri: in silico structural and functional studies.
Biochem Biophys Res Commun. 2011 Nov 18;415(2):229-34. doi: 10.1016/j.bbrc.2011.09.116. Epub 2011 Oct 1. PMID: 21982766.
9. Choong YS, Lim TS, Chew AL, Aziah I, Ismail A. Structural and functional studies of a 50 kDa antigenic protein from Salmonella enterica serovar Typhi. J Mol Graph Model. 2011 Apr;29(6):834-42. doi: 10.1016/j.jmgm.2011.01.008. Epub 2011 Mar 2. PMID: 21371926.
10. Wahab HA, Choong YS, Ibrahim P, Sadikun A, Scior T. Elucidating isoniazid resistance using molecular modeling. J Chem Inf Model. 2009 Jan;49(1):97-107. doi: 10.1021/ci8001342. PMID: 19067649.
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