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Welcome to the Computational Biology and Bioinformatics Lab at University of Macau
Molecular interactions play a pivotal role in all life processes. They are also central to the development of many applications in the field of drug design and nanotechnology. In our lab, our researches focus on developing computational techniques to model and to understand molecular interactions at interfaces, which include protein-ligand, protein-protein, protein-membrane, and protein-nanomaterial.Seminar: "Sinotools: a computational framework to analyze cancer genomic sequencing data for precision oncology"
updated: 20 Sep 2019
Speaker: Prof. Bingding HUANG (College of Big Data and Internet, Shenzhen University)
Date: 19/09/2019
Time: 2:30PM -3:30PM
Venue: E12-G004 (University of Macau)
Congratulations to Faraz!
updated: 22 Aug 2019
Faraz Mohammadali Shaikh, a PhD student from the Faculty of Science and Technology (FST), University of Macau (UM), recently discovered two Ebola virus drug candidates. The groundbreaking discovery has been validated by collaborators from the University of Oxford through biological experiments, attracting international attention. Shaikh was awarded the Carl Storm International Diversity Fellowship, which sponsored him to attend the 2019 Computer-Aided Drug Design Gordon Research Seminar (GRS) and the 2019 Computer-Aided Drug Design Gordon Research Conference (GRC) in the United States to present his findings, in order to help the medical industry develop more anti-Ebola drugs.
Seminar: "Computational protein design by accommodating flexibility and binding free energy in improving the affinity"
updated: 27 July 2019
Speaker: Prof. Vannajan Sanghiran Lee (University of Malaya, Malaysia)
Date: 26/07/2019
Time: 3:00PM -4:00PM
Venue: E11-405 (University of Macau)
Chinese New Year Gathering Dinner
updated: 9 Feb 2018
At the Thai Palace restaurant near to Ponte 16, Macau. Yummy food with good price. What is missing is Faraz....(Left to right, anticlockwise: Giotto, Michael, Jimmy, Yan, Pratiti and Shirley) Wish for good health, good life and good career in the Year of Dog)
Pratiti's and Yan's papers got accepted! Congratuations.
updated: 10 Jan 2018
Thanks to all the hard work of Pratiti and Yan. This is perhaps the best gift at the beginning of the year: AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest, accepted by Scientific Reports
Open positions
updated: 02 Jun 2017
- One-year Research Assistant (RA) for Bioinformatics project (see Vacancy page)
- One-year Research Assistant (RA) for Molecular Biology experiment (see Vacancy page)
Faraz's research trip to University of Oxford for the Ebola project is on the news
updated: 28 Sep 2016
Our PhD student Faraz Shaikh is currently on a research trip at the Unversity of Oxford, joining the research project about drug design for Ebola virus. Faraz will apply advanced molecular docking and lead optimization techniques as well as molecular dynamics simulations to find few potential lead molecules that can bind effectively to the recently discovered binding pocket at the Ebola glycoprotein by the same group. Faraz, good work and good luck!
References:
Master thesis topics offered
updated: 23 Aug 2016
We are offering three new master thesis topics, for both academic thesis and applied thesis to the master students of Department and Computer Information Science, FST. For details, please read the VACANCY page.
Congratulation to Wendy for Best Project award
updated: 3 Jun 2016
Wendy's work on developing mobile controller for the PyMOL molecular visualization software has been awarded as one of the best bachelor final year projects this year. And now she is heading for her new job in Macau, all the best.
Press release
updated: 29 Apr 2016
Press release of this work at UM news, Macao Daily News and other local newspapers.
Congratulations to Faraz, Jimmy, Giotto & Allan
updated: 28 Apr 2016
Three papers, one by Faraz, one by Jimmy and one by Giotto & Allan have been accepted recently. Thanks for your great effort!!
Computational
Studies of the Human Complement Component 5A Receptor: Identifying
Novel Natural Compound Inhibitors by Homology Modeling and Virtual
Screening
Fara Shaikh and Shirley W. I. Siu* (accepted to publish in Medicinal
Chemistry Research)
ProtPOS: A Python Package for the
Prediction of Protein Preferred Orientation on a Surface
Jimmy C. F. Ngai, Pui-In Mak, and Shirley W. I. Siu*
(accepted to publish in Bioinformatics)
Improving the Efficiency of
PSOVina for Protein-Ligand Docking by Two-Stage Local Search
Hio Kuan Tai, Hang Lin, and Shirley W. I. Siu* (accepted by WCCI2016/CEC2016)
CBBio at new UM Campus
updated: 24 Sep 2015
In front of the FST E11 building
stone
From left, 2nd row: Allan, Jimmy, Shirley, Faraz, Michael
1st row: Wendy and Giotto
This is the first time ever that I feel our team is "in shape".
From left, 2nd row: Allan, Jimmy, Shirley, Faraz, Michael
1st row: Wendy and Giotto
This is the first time ever that I feel our team is "in shape".
Inside the FST building
In front of our lab E11-1048, which is still under some construction. Looking foward to move-in in Oct.
Open positions
Post-doctoral position in Computational Chemistry or Computational Biology
updated: 09 Jul 2015
- Description: The Computational Biology and Bioinformatics Group at the University of Macau is looking for a post-doctoral candidate in the area of computational chemistry or computational biology to participate in an interdisciplinary research project. The key research goal of the project is to study the protein-surface adsorption process on biotechnologically relevant surfaces such as Teflon using coarse-grained molecular dynamics (CGMD) simulations. The work includes modeling of interested system, parameterization, simulation and analysis. Applicants should have knowledge in MD techniques and programming, have received their Ph.D. recently with training in computational chemistry, computational biology or related areas, and a significant track record.
- Duration: Nov 2015 - Oct 2016, with possibility for renewal subject to work performance and funding availability
- To apply: Interested applicants should email Dr. Shirley Siu a curriculum vitae that includes personal information, education, a list of publications, statement of research interests (~2 pages), academic transcripts, and contact information for three references.
- Contact:
Dr. Shirley Siu at
Fast Docking Software PSOVina 1.0 is released
updated: 27 Jan 2015
The first version of our open-source fast docking tool PSOVina is released. It uses the particle swarm optimization (PSO) technique to quickly search for the optimal docking pose of a ligand based on the AutoDock Vina framework. Our tests show that PSOVina docks 51-60% shorter in time.
Awards
The bachelor project "Improving Protein-Ligand Docking by Particle Swarm Optimization" by Marcus Ng has been awarded as one of the five best final year projects in the CIS department and made into the Dean's Final Year Project List of 2013/2014. Congratuations to Marcus!!
updated: 30 June 2014
updated: 2 Jun 2017
Our works have been supported by the following research grants:
- 1/2013-12/2014 - "Protein-ligand Binding Affinity Prediction for Structure-Based Drug Design", SRG022-FST13-SWI, Research Committee of University of Macau, MOP 100,000 (PI)
- 4/2014-3/2017 - "Computational Modeling of Electric Field in Digital Microfluidic Technologies and its Application on Simulating Droplets and Protein Adsorption on Device Surfaces", MYRG2014-00104-FST, Research Committee of University of Macau, MOP 835,000 (PI)
- 4/2015-3/2018 - "Improving Flexible Receptor Protein-Ligand Docking for Structure-Based Drug Design by Swarm Intelligence Algorithms", MYRG2015-00212-FST, Research Committee of University of Macau, MOP 1,072,000 (PI)
- 1/2018-31/12/2020 - "Structure, Function, and Natural Compound Inhibitor Identification of the Inflammatory Complement C5a Receptors by Combined In Silico and In Vitro Methods", MYRG2017-00146-FST, Research Committee of University of Macau, MOP 1,492,500 (PI)
- 5/4/2017 - 4/4/2019 - "Investigation of Staphylococcus Aureaus Protein A Adsorption on Mixed Self-Assembled Monolayers for Biosensor Development Using Computer Simulations", 066/2016/A, Science and Technology Development Fund, Macao S.A.R. (FDCT), MOP 351,850 (PI).