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Studying phase transition temperature of pentadecane using MD simulations

Vacancies 

Annoucement of job vacancies and available thesis topics

Please contact Dr. Shirley Siu at  if you are interested in working with us or doing a thesis in the lab. We also welcome new topic ideas related to computational biology and bioinformatics.






Bioinformatics Research Assistant (full-time, Jan 2018-)

Updated: 2 Jun 2017

We are seeking motivated applicants for a full-time RA position at Computational Biology and Bioinformatics lab (CBBIO) at University of Macau (UM). The successful applicant will contribute to a funded project that will construct a comprehensive natural product database for faciliating structure-based drug design. 

Duties include, but are not limited to, data mining, data curation, data analysis, database design, website development, and manuscript writing.

Basic qualifications:  Master/PhD degree with training in Bioinformatics or in Computer Science but strong interests in bioinformatics with experience. Candidate is expected to be familiar with programming with Cheminformatics libraries, in particular RDKit, ChemmineR, OpenBabel, and drug design related software such as Schrodinger, AutoDock and AutoDock Vina, GROMACS.  

Submission: Please send the following items to (shirleysiu at umac dot mo): (1) A letter describing your interests, skills, and prior research experience; (2) Curriculum vitae; (3) Academic reports and certificates; (4)  At least 2 reference letters

Application is opened until position is filled. 

Initial contract is for one-year, starting in Jan 2018. 

Contract renewal is subject to performance and fund availability.

Molecular Biology Research Assistant (full-time, Nov 2018-)

Updated: 2 Jun 2017

We are seeking motivated applicants for a full-time RA position at Computational Biology and Bioinformatics lab (CBBIO) at University of Macau (UM). The successful applicant will contribute to a funded project in inhibitor identification of the C5aR receptors for inflammatory diseases.

Duties include, but are not limited to, the preparation, execution and analysis of biological assays to investigate activities of ligands against the targets, and manuscript writing.

Basic qualifications:  Master/PhD degree with training in Molecular Biology. Prior experiences with binding assays, intracellular calcium mobilization assay, chemotaxis assay, reactive super oxide species generation assay, c-AMP assay, interleukin and cytokines assays, multi caspase assay, and microarray based global transcriptome profiling are preferred.

Submission: Please send the following items to (shirleysiu at umac dot mo): (1) A letter describing your interests, skills, and prior research experience; (2) Curriculum vitae; (3) Academic reports and certificates; (4)  At least 2 reference letters

Application is opened until position is filled. 

Initial contract is for one-year, starting in Nov 2018  

Contract renewal is subject to performance and fund availability.

CS Master Thesis Topics

Suitable for CS/E-commerce master students from FST

1. Evaluation of MM-PBSA free energy calculation methods for small molecule binding to C5aR (Applied thesis)
MM-PBSA (Molecular Mechanics Poisson−Boltzmann Surface Area) method calculates binding energy of biomolecular associations such as protein-protein, protein-ligand protein-DNA, etc. The energy values should be accurate enough such that they can be directly compared to experimental measures.  Recently there are releases of two such tools: g_mmpbsa and GMXPBSA 2.1, both of them use APBS for solving the Poisson-Boltzmann equations and aim to streamline the calculation from molecular dynamics data.

In this project, we will apply these tools on binding affinity calculation of known and novel ligands in the Human Complement 5 Receptor (C5aR) protein, a crucial protein in our body immune defence system which is also a novel pharmacological target in drug discovery recently.  Both programs will be studied in detail about their input and output data, as well as comparing their prediction performance using experimental data.  

Required skills:
None, but interest in computational drug design would be a plus.

References:
1. g_mmpbsa—A GROMACS Tool for High-Thoughput MM-PBSA Calculations (2014) Rashmi Kumari, Rajendra Kumar, and Andrew Lynn Journal of Chemical Information and Modeling 54 (7), 1951-1962.
2. GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning (2015) C. Paissonia, D. Spiliotopoulosa, G. Muscoa, A. Spitaleri. Computer Physics Communications 186, 105–107.

Keywords: MM-PBSA, free energy, binding affinity, GROMACS