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Welcome to
the Computational Biology
and Bioinformatics Lab
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. Updated: 22 Oct 2022
This webpage will no longer be updated. Please follow our research at the University of Saint Joseph:
- CBBio team & PI
- Our Bioinformatics Web Server to access our antimicrobial and anticancer peptide prediction tools, ligand-target identification tool, chemical compound toxicity prediction tools.
See you there~~~
Call for Papers [Antibiotics IF 4.639] Special Issue “Antimicrobial Peptides – Discovery, Structure, Function, and Application
Updated: 30 Dec 2021
Together with Prof. Campbell-Valois, Prof. Shoombuatong, and Dr. Jusoh, we are editing the Special Issue in the journal Antibiotics, focusing on the discovery and characterization of antimicrobial peptides with applications:
The emergence of multidrug-resistant bacteria (MDR) has become a global health crisis, affecting our ability to treat infectious diseases and leading to increasing morbidity and mortality. New treatment options are therefore urgently needed to eradicate MDR bacteria. Among them, antimicrobial peptides (AMPs) are emerging as promising antibiotic agents due to their remarkable broad-spectrum antibacterial properties and lower probability of bacterial resistance development. To date, more than 3000 AMPs have been discovered from nature, and many more chemically modified synthetic peptides with improved biological activities have been developed. Nevertheless, the successful translational applications of AMPs are very limited. On the one hand, our incomplete understanding of how these peptides work hinders their development into therapeutics. On the other hand, the relatively high production costs, short half-life, low bioavailability and potential toxic side effects of AMPs compared to conventional small molecule drugs make them less attractive to study through the established drug discovery pipeline. Addressing these challenges requires a deeper understanding of AMPs and innovative techniques to discover and design potent AMPs that are relevant to clinical applications.
In this Special Issue, we aim to collect and disseminate the latest experimental and computational works on the discovery and characterization of AMPs, in terms of their structures, functions and potential applications. Manuscripts from original research and review articles are invited. Submitted manuscripts will be peer-reviewed to ensure high quality of contributions in this issue.
Submissions are welcome! Click to see Special Issue -- Antimicrobial Peptides: Discovery, Structure, Function, and Application more in details.
Three papers recently accepted!
Updated: 30
Nov 2021
Our two works have recently accepted by Journal of Cheminformatics and Journal of Chemical and Information Modeling. Plus a collaboration work with the ICMS team of Simon Lee on toxic peptides, accepted by Frontiers in Pharmacology. Congratuations to Ray and Simon!!
And importantly, our two online services AcPEP for anticancer peptide classification and anticancerous activity prediction, SSL-GCN for chemical toxicity prediction for 12 toxicological endpoints are now online at app.cbbio.online!
Move notification & call for
new team members
Updated: 23
Jul 2021
I am thrilled to announce that I will join the Institute
of Science and Environment (ISE) at University
of Saint Joseph (Macao) in September. I am looking forward
to working with my biologist, ecologist, and geologist
colleagues on interdisciplinary research to advance science
while also benefiting Macao society.
As I am developing a new research team in the Computational
Biology and Artificial Intelligence area, you are welcome to
join me/us in this interesting and challenging research journey.
Feel free to email me at siuwengin_at_gmail.com to discuss.
To kick start, here is our call for a postdoctoral candidate to
participate in the applied project that will be proposed to
FDCT/Macau for funding: LinkedIn,
Facebook,
JobRxiv
Furthermore, a new lab page will be setup in the near future.
However, this CBBio website will remain for a while to continue
sharing all our research outputs funded by UM.
Congratulation to Ray
completion of his master's study
Updated: 23
Jul 2021
Ray gave his defense in June and finally all remaining works are
done! Today, he arrived back to his hometown and will prepare
for the next journey -- PhD in Bioinformatics in the Central
Institute of Mental Health (CIMH), Germany. Can't be more
excited than that. All the best to his visa application process!
The new location for our apps: https://app.cbbio.online
Updated: 24 Jun 2021
We have moved our three online prediction services to the new
web server, which provides better security and faster
access:
Antimicrobial peptide prediction AxPEP
Anticancer peptide prediction AcPEP
Chemical toxicity prediction BESTox
The xDeep-AcPEP paper is
accepted!
Updated: 23
Jun 2021
Congratulations to Ray and Carter!! The anticancer peptide
prediction paper has just accepted by Journal of Chemical
Information and Modeling. Well done! Of course, the server
cannot be possible without the help of Edison to help setting up
the new server!
The LigTMap paper is accepted!
Updated: 29
May 2021
Congratulations to Faraz, Nirali, Giotto!! Our ligand target
prediction method is accepted for publication by the Journal of
Cheminformatics!
LigTMap server and
source code are now opened access
Updated: 20 Feb 2021
Our ligand and structure-based small
molecule target and activity prediction method LigTMap is
released as a server for easy access. The source code is
also available at GitHub
and the method preprint is at ChemRixv.
Domain moved
Updated: 21 Oct 2020
Our server is online again, with a new domain https://cbbio.online. We will
continue to share our research work here.
Congratulations to
Dr. Faraz
Updated: 05 May 2020
Our PhD student Faraz Shaikh has successfully passed the defense
today. Congratulations to Dr. Faraz!!
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
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).
