Aim and Objective

My vivid interest dwells in gaining a detailed understanding of macro-molecular interaction as a basis of their sequence, structure and function, through the application and integration of Omics and biophysical approaches. Hence to develop new or improve existing models that better explain drug pathway interaction with disease. I have built my skills and expertise in elucidating the molecular interaction through the application of Structural Bioinformatics approaches not limited to computational modeling (all atom and Course grained molecular dynamics simulations), free energy perturbation but also macro molecular modeling and docking (ligand based and structure based docking).

Selected work

Integrating Multi-Omic Approaches to Unveil the Underlying Molecular Mechanisms of Disease

Development of Predictive Models to better explain Biological processes.
Modeling of Membrane protein Systems: Lactose Permease System:
Membrane protein transporters govern important cellular processes and are therefore central to human health. To accomplish transport, these proteins rearrange their structures to alternatively expose an internal binding site to either side of the membrane. However, to understand the underlying transport mechanism, the molecular details of the interactions between the protein and the transported compound need to be determined.
Thus To Determine the molecular factors that govern the specificity and affinity of substrates, the application of molecular dynamics approaches as well as enhanced sampling to capture the underlying details of interactions were utilized.
Key Words: Molecular Dynamics, Drug discovery, Omics, Enhanced Sampling, Docking, protein-protein | protein-ligand interaction, Enzyme Kinetics, Free Energy Perturbation.

Drug Repurposing | Virtual Screening | Optimization of Lead Compounds

Drug Repurposing and Molecular drug Screening for Identification of Dual-Inhibitors for VEGFR/c-Met Receptors in cancer.
Virtual Drug Screening: Kinase Receptors:
c-Met and VEGFR2 kinase have emerged as a promising target for cancer drug development. We are currently using biophysical approaches (MMPBSA, Docking and MD) to screen and test for dual inhibitors for the two kinase receptors.
Thus

Exploration of the ligand-receptor recognition pathway (Extension of the supervision algorithm to standard simulation protocol) (SuMD). To characterize the binding and unbinding events in the protein ligand complex. SMD in Gromacs and visualization of the applied energy terms in xmgrace. Thus, quantifying the energetic profiles in the transport pathway. Protein-ligand interaction energy using Umbrella sampling and MM/PBSA energy quantification.

Pocketomics: Identification of the binding sites by studying the geometric properties of the protein Pockets. Cavities are identified by way of weighted Delaunay triangulation and applying the alpha complex for shape measurements.

STUART LUTIMBA, | Research Assistant

National Tsing Hua University, Taiwan

Computational Biology Laboratory

Institute of Bioinformatics and Structural Biology,

101, Sec 2, Kuang-Fu Rd., Hsinchu, Taiwan, R.O.C.

Contact: +886909147106

Skype: lutimba.stuart

lutimbastuart@gapp.nthu.edu.tw | lutimbastuart@mx.nthu.edu.tw | lutimba.stuart@yahoo.com

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