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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. 

We have moved!
Updated: 22 Oct 2022

This webpage will no longer be updated. Please follow our research at the University of Saint Joseph:

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!

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 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:
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 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

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!


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".

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

position in Computational Chemistry or Computational Biology  
Updated: 09 Jul 2015

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.

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!!

Visit the faculty news page for details
Updated: 30 June 2014
Project Funding
Updated: 2 Jun 2017
Our works have been supported by the following research grants: