email 1: shirley.siu at
email 2: siuwengin at

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Keywords: Computer-Aided Drug Design, Molecular Docking, Cheminformatics, Molecular Dynamics, Force Field, Machine Learning, Deep Learning, Optimization Algorithms, Therapeutic Peptides (AMP, ACP), Drug Target Prediction, GPCR, Ion Channels

Associate Research Professor
Institute of Science and Environment
University of Saint Joseph

PhD (Dr. rer. nat.) in Computational Biology, Saarland University, Germany
MSc in Computational Molecular Biology, Saarland University & Max-Planck Institute for Computer Science, Germany
MSc/BSc in Software Engineering, University of Macau, Macau

  • Visiting PhD researcher, Jane Cai, currently a PhD candidate in the Macao Polytechnic University, has joined our team to explore how to use the latest deep learning methods to predict antimicrobial peptides

Our mission

Our mission is to improve computational methods for accelerating the drug discovery and development process. We have been developing bioinformatics tools that enable researchers to solve critical drug discovery problems including protein-ligand binding (PSOVina, GWOVina), drug target identification (LigTMap), biological activity (AxPEP, AcPEP) and toxicity predictions (BESTox, SSL-GCN). Our previously developed methods can be accessed directly online via this apps portal ( Some program source codes can be downloaded from my Github page or SourceForge page.

Guest-editing journal

Topic Editors: Shira Lynn Broschat (Washington State University), Shirley Siu (USJ), Cesar de la Fuente-Nunez (University of Pennsylvania)

Bioactive Peptide Prediction Tools

Antimicrobial Peptide Prediction v1.0 (old)
Antimicrobial Peptide Prediction v2.0
Anticancer Peptide Prediction

Small Molecular Chemical Prediction Tools

Drug-Protein Target Prediction
Simple Chemical Toxicity Prediction
Graph-Based Chemical Toxicity Prediction

Molecular Docking Tools



Jielu Yan
PostDoc Researcher
PhD student, Dept of Computer and Information Science, University of Macau
(2018 – 2023)
MSc Computer Science, University of Macau (2018)
Interests: Machine learning and deep Learning of bioactive peptides
Jianxu Cai
Visiting PhD Researcher
PhD student, Faculty of Applied Sciences, Macao Polytechnic Institute (2022 – present)
MSc Computer Science, University of Macau (2022)
Interests: Generative modeling of bioactive peptides


To date, drug discovery has been a major challenge due to limited knowledge of disease and difficulty in identifying the right molecular targets and drug candidates. Our research focuses on developing computational algorithms to support drug discovery by using bioinformatics methods, machine learning and optimisation algorithms. In particular, we have developed molecular docking programs to identify native binding modes of proteins, peptides, and small molecular compounds. Recently, we have also become interested in therapeutic applications of peptides (antimicrobial, anticancer, GPCR interacting, ion channel interacting) by studying the relationship between peptide molecular properties and biological activities observed in experiments. We work on modelling and simulation of proteins to study their structures and dynamics and to understand their functions. We have been involved in the development of membrane lipid force fields and more recently in the modelling of self-assembling monolayers on biochips.


AMPSEC, an AntiMicrobial Peptides SECretion platform to identify alternatives to antibiotics
PI: Prof. F-X Campbell-Velois, Co-PI: Shirley Siu
2022.4-2024.3 *active*
Grant no.: NFRFE-2021-00913



  • Yan, J.; Zhang, B.; Zhou M.; Campbell-Valois, F-X.; Siu, Shirley W. I.* A deep learning method for predicting the minimum inhibitory concentration of antimicrobial peptides against Escherichia coli using Multi-Branch-CNN and Attention. mSystems. 2023, e0034523. doi:10.1128/msystems.00345-23
  • Qin, Haixin; Zuo, Weimin; Ge, Lilin; Siu, Shirley W. I. ; Wang, Lei; Chen, Xiaoling; Ma, Chengbang; Chen, Tianbao; Zhou, Mei; Cao, Zhijian; Kwok, Hang Fai. Discovery and Analysis of a Novel Antimicrobial Peptide B1AW from the Skin Secretion of Amolops Wuyiensis and Improving the Membrane-binding Affinity through the Construction of the Lysine-introduced Analogue. Computational and Structural Biotechnology Journal 2023
  • Lei, Thomas M. T.; Ng, Stanley C. W.; Siu, Shirley W. I.* Application of ANN, XGBoost, and Other ML Methods to Forecast Air Quality in Macau. Sustainability 2023, 15, 5341.


  • Yan, J.; Cai, J.; Zhang, B.; Wang, Y.; Wong, D.F.; Siu, Shirley W. I.* Recent Progress in the Discovery and Design of Antimicrobial Peptides Using Traditional Machine Learning and Deep Learning. Antibiotics 2022, 11, 1451.
  • Lei, Thomas M. T.; Siu, Shirley W. I.; Joana Monjardino; Luisa Mendes; and Francisco Ferreira. Using Machine Learning Methods to Forecast Air Quality: A Case Study in Macao. Atmosphere 2022, 13, 1412.
  • Yan, J.; Zhang, B.; Zhou, M.; Kwok, H.F.; Siu, Shirley W. I.* Multi-Branch-CNN: classification of ion channel interacting peptides using multi-branch convolutional neural networks. Computers in Biology and Medicine, 2022, 147, 105717.
  • Chen, Qian; Liang, Zirong; Yue, Qian; Wang, Xiufen; Siu, Shirley W. I.; Pui Man Hoi, Maggie; Lee, Simon. A neuropeptide Y/F-like polypeptide derived from the transcriptome of Turbinaria Peltata suppresses LPS-induced astrocytic inflammation. Journal of Natural Products, 2022, 85, 6, 1569-1580.
  • Chen, Hanbin; Siu, Shirley W. I.; Wong, Clarence Tsun Ting; Qiu, Jianwen; Cheung, Alex Kwok Kuen; Lee, Simon Ming Yuen. Anti-epileptic Kunitz-like peptides discovered in the branching coral Acropora digitifera through transcriptomic analysis. Archives of Toxicology, 2022,
  • Bijani, Sabera; Shaikh, Faraz; Mirza, Sheefa; Siu, Shirley W. I.; Jain, Nayan; Rawal, Rakesh; Richards, Nigel G. J.; Shah, Anamik; Radadiya, Ashish. Novel dihydropyrimidinone derivatives as potential P-glycoprotein modulators.  ACS Omega, 2022, 7, 19, 16278-16287.
  • Chen, Jiarui; Si, Yain-Whar; Un, Chon-Wai; Siu, Shirley W. I.* Chemical Toxicity Prediction Based on Semi-supervised Learning and Graph Convolutional Neural Network. Journal of Cheminformatics 2021, 13: 93.
  • He, Qi-Qiao; Siu, Shirley W. I.; Si, Yain-Whar. Instance-based deep transfer learning with attention for stock movement prediction. Applied Intelligence, 2022
  • He, Qi-Qiao; Siu, Shirley Weng In; Si, Yain-Whar. Attentive recurrent adversarial domain adaptation with top-k pseudo-labeling for time series classification. Applied Intelligence 2022,




  • Bhadra, Pratiti and Siu, Shirley W. I.* Refined empirical force field to model protein-self assembled monolayer interactions based on AMBER14 and GAFF. Langmuir 2019, 35, 29, 9622-9633. ESI-Q1
  • Liao, Q.; Gong, G.; Poon, T. C. W.; Ang, I. L.; Lei, K. M. K.; Siu, Shirley W. I; Wong, C. T. T.; Rádis-Baptista, G.; Lee, M. Y.. Combined transcriptomic and proteomic analysis reveals a diversity of venom-related and toxin-like peptides expressed in the mat anemone zoanthus natalensis (cnidaria, hexacorallia). Archives of Toxicology 2019, 93, 1745-1767. JCR-Q1
  • Shaikh, Faraz; Zhao, Yuguang ; Alvarez, Luis; Iliopoulou, Maria; Lohans, Christopher; Schofield, Christopher; Padilla-Parra, Sergi ; Siu, Shirley W. I.; Fry, Elizabeth; Ren, Jingshan; Stuart, David. Structure-based in silico screening identifies a potent Ebolavirus inhibitor from a traditional chinese medicine library. Journal of Medicinal Chemistry 2019, 62, 2928-2937. JCR-Q1


  • Tai, Hio Kuan; Jusoh, Siti Azma; Siu, Shirley W. I.* Chaos-embedded particle swarm optimization approach for protein-ligand docking and virtual screening. Journal of Cheminformatics 2018, 10, 62. JCR-Q1
  • Lin, Hang and Siu, Shirley W. I.* (2018) A hybrid cuckoo search and differential evolution approach to protein-ligand docking. International Journal of Molecular Sciences, 19 (10), 3181. ESI-Q1
  • Liao, Q.; Li, S.; Siu, Shirley W. I.; Morlighem, J.-É. R. L.; Wong, C. T. T.; Wang, X.; Rádis-Baptista, G.; Lee, M.-Y.. Novel neurotoxic peptides from Protopalythoa variabilis virtually interact with voltage-gated sodium channel and display anti-epilepsy and neuroprotective activities in zebrafish. Archives of Toxicology 2018, 93, 189-206. JCR-Q1
  • Shaikh, F.; He, J.; Bhadra, P.; Chen, X.Siu, Shirley W. I. (2018) TNF receptor type II as an emerging drug target for the treatment of cancer, autoimmune diseases, and graft-versus-host disease: Current perspectives and in silico search for small molecule binders. Frontiers in Immunology 2018 9, 1382. ESI-Q1
  • Liao, Q.; Gong, G.; Siu, Shirley W. I.; Wong, C. T. T.; Tse, Y. C.; Rádis-Baptista, G.; Lee, M.-Y. A novel ShK-like toxic peptide from the transcriptome of the cnidarian Palythoa caribaeorum displays neuroprotection and cardioprotection in zebrafish. Toxins 2018, 10 (6): 238. JCR-Q1
  • Duan, K.; Fong, S.Siu, Shirley W. I.; Song, W.; Guan, S. S.-U. Adaptive incremental genetic algorithm for task scheduling in cloud. Symmetry 2018 10 (5), 168.
  • Liao, Q.; Li, S.; Siu, Shirley W. I.; Yang, B.; Huang, C.; Chan, J.; Morlighem, J.-É.; Wong, C.; Radis-Baptista, G.; Lee, M.-Y. Novel Kunitz-like peptides discovered in the zoanthid Palythoa caribaeorum through transcriptome sequencing. Journal of Proteome Research 2018, 17 (2), 891-902. JCR-Q1
  • Bhadra, P.; Yan, J.; Li, J.; Fong, S.; Siu, Shirley W. I.* AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest. Scientific Reports 2018, 8, 1697. JCR-Q1


  • Bhadra, P.; Siu, Shirley W. I.* Comparison of biomolecular force fields for alkanethiol self-assembled monolayer simulations. Journal of Physical Chemistry C 2017, 121 (47), 26340-26349 JCR-Q1
  • Cao, H.; Ng, M. C. K.; Jusoh, S. A.; Tai, H. K.; Siu, Shirley W. I.* TMDIM: An improved algorithm for the structure prediction of transmembrane domains of bitopic dimers. Journal of Computer Aided Molecular Design 2017, 31, 855-865.


  • Chan, H. K.; Mak, P. I.; Siu, Shirley W. I.* Exploring the behavior of water nanodroplet on a coplanar electrowetting-on-dielectric: A molecular dynamics approach. Micro & Nano Letters 2017, 12 (7), 486-489.
  • Lam, W. W. T.; Siu, Shirley W. I.* PyMOL mControl: Manipulating molecular visualization with mobile devices. Biochemistry and Molecular Biology Education 2017, 45(1), 76-83.
  • Shaikh, F.; Siu, Shirley W. I.* Identification of novel natural compound inhibitors for human complement component 5A receptor by homology modeling and virtual screening. Medicinal Chemistry Research 2016, 25, 1564-1573.
  • Ngai, J. C. F.; Mak, P. I.; Siu, Shirley W. I.* ProtPOS: A python package for the prediction of protein preferred orientation on a surface. Bioinformatics 2016, 32, 2537-2538. JCR-Q1


  • Ng, M. C. K.; Fong, Simon; Siu, Shirley W. I.* PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking. Journal of Bioinformatics and Computational Biology 2015, 13 (3), 1541007. Most Read and Most Cited Paper in JBCB
  • Wang, R.; Zhou, H.; Siu, Shirley W. I.; Gan, Y.; Wang, Y.; Ouyang, D.* Comparison of three molecular simulation approaches for cyclodextrin-ibuprofen complexation. Journal of Nanomaterials 2015, Article ID 193049. ESI-Q1
  • Fong, S.*; Liang, J.; Siu, Shirley W. I.; Chan, J. H. Efficient variation-based feature selection for medical data classification. Journal of Medical Imaging and Health Informatics 2015, 5, 1093-1098.
  • Fong, S.*; Siu, Shirley W. I.; Zhou, S.; Chan, J. H.; Mohammed, S.; Fiaidhi, J. Real-time analysis of vital signs using incremental data stream mining techniques with a case study of ARDS under icu treatment. Journal of Medical Imaging and Health Informatics 2015, 5, 1108-1115.


  • Siu, Shirley W. I.; Pluhackova, K.; Böckmann, R. A.* Optimization of the OPLS-AA force field for long hydrocarbons. Journal of Chemical Theory and Computation 2012, 8, 1459-1470. JCR-Q1
  • Borisovska, M.; Schwarz, Y. N.; Narzi, D.; Siu, Shirley W. I.; Kesavan, J.; Mohrmann, R.; Böckmann, R. A.; Bruns, D.* Membrane-proximal tryptophanes of synaptobrevin II stabilize priming of secretory vesicles. Journal of Neuroscience 2012, 32, 15983-15997. JCR-Q1


  • Wang, L.; Siu, Shirley W. I.; Gu, W.; Helms, V.* Downhill binding energy surface of the barnase-barstar complex. Biopolymers 2010, 93, 977–985.
  • Jusoh, S. A.; Welsch, C.; Siu, Shirley W. I.; Böckmann, R. A.; Helms, V.* Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. Journal of Molecular Modeling 2010, 16, 1625-1637.


  • Siu, Shirley W. I.; Böckmann, R. A.* Low free energy barrier for ion permeation through double-helical gramicidin. Journal of Physical Chemistry B 2009, 113, 3195-3202. ESI-Q1
  • Vacha, R.; Siu, Shirley W. I.; Petrov, M.; Böckmann, R. A., Barucha-Kraszewska, J.; Jurkiewicz, P.; Hof, M.; Berkowitz, M. L.; Jungwirth, P.* Effects of alkali cations and halide anions on the DOPC lipid membrane. Journal of Physical Chemistry A 2009, 113, 7235-7243. ESI-Q1


  • Narzi, D.; Siu, Shirley W. I.; Stirnimann, C. U.; Grimshaw, J. P.A.; Glockshuber, R.; Capitani, G.; Böckmann, R. A.* Evidence for proton shuffling in a thioredoxin-like protein during catalysis. Journal of Molecular Biology 2008, 382, 978-986. JCR-Q1
  • Siu, Shirley W. I.; Vacha, R.; Jungwirth, P.; Böckmann. R. A.* Biomolecular simulations of membranes: Physical properties from different force fields. Journal of Chemical Physics 2008, 128, 125103. Selected for April issue of Virtual Journal of Biological Physics Research. ESI-Q1


  • Siu, Shirley W. I. and Böckmann, R. A.* Electric field effects on membranes: gramicidin A as a test ground. Journal of Structural Biology 2007 157, 545-556. JCR-Q1


  • Antes, I.+*; Siu, Shirley W. I.+; Lengauer, T. DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics 2006, 22 (14), e16-e24. JCR-Q1 +equal contributions 


  1. Cai, J.; Wang, Y. and Siu, Shirley W. I.* Protein-based data augmentation for the prediction of peptide toxicity using deep learning. In Proceedings of International Conference of Bioinformatics and Computational Biology (ICBCB 2023), Conference Proceedings by IEEE, ISBN: 978-1-6654-0108-1.
  2. Chen, J.; Cheong, H. H and Siu, Shirley W. I.* BESTox: A convolutional neural network regression model based on binary-encoded SMILES for acute oral toxicity prediction of chemical compounds. In: Martín-Vide C., Vega-Rodríguez M., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2020. Lecture Notes in Computer Science, vol 12099. Springer, Cham
  3. Ao, M. C. and Siu, Shirley W. I.* Evaluating variants of firefly algorithm for ligand pose prediction in protein-ligand docking program. In Proceedings of the 12th International Conference on Bioinformatics and Biomedical Technology (ICBBT2020), accepted.
  4. Gao, L. and Siu, Shirley W. I.* Study of data imbalanced problem in protein-peptide binding prediction. In Proceedings of the 12th International Conference on Bioinformatics and Biomedical Technology (ICBBT2020), accepted.
  5. Tai, H. K.; Lin, H.; Siu, Shirley W. I.* Improving the efficiency of psovina for protein-ligand docking by two-stage local search. In the Proceeding of the 2016 IEEE Congress on Evolutionary Computation (CEC2016), Vancouver, Canada, July 24-29, 2016.
  6. Ngai, J. C. F.; Mak, P. I.; Siu, Shirley W. I.* Predicting favorable protein docking poses on a solid surface by particle swarm optimization. In the Proceedings of the 2015 IEEE Congress on Evolutionary Computation (CEC2015), 2745-2752, Sendai, Japan, May 25-28, 2015.
  7. Siu, Shirley W. I.; Wong, T. K. F.; Fong, S. Comparison of cutoff strategies for geometrical features in machine learning-based scoring functions. Proceedings of the 9th International Conference on Advanced Data Mining and Applications (ADMA2013), Hangzhou, China, December 14-16, 2013, LNAI 8347, 336-347, Springer, 2013.
  8. Wang, R.; Siu, Shirley W. I.; Böckmann, R. A. Fine-grained protein mutation extraction from biological literature. Proceedings of International Conference on Electronic Computer Technology (ICECT-2009), Macau, 2009.
  9. Leung, A.; Fong, S.; Siu, Shirley W. I. Smart card-based irregular access patterns detection system. IEEE International Conference on e-Technology, e-Commerce and e-Service (EEE 2004), Taipei, Taiwan, 28-31 March 2004, pp.546-553.
  10. Fong, S.; Siu, Shirley W. I. An integrative framework of predictive mining methods for medical prognosis. IASTED the 2nd International Conference on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 16-18 February 2004.
  11. Fong, S.; Siu, Shirley W. I.; Sun, A. Market watcher agent for e-commerce. IASTED the International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004.
  12. Leung, A.; Fong, S.; Siu, Shirley W. I. Smart card-based identification and access control model with real-time suspicious action detection mechanism. IASTED The International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004.
  13. Siu, Shirley W. I.; Fong, S.; Guo, Z. S.; Si Tou, K. F. Context-aware for service discovery in ad hoc environment. IASTED Intl. Conf. on Wireless and Optical Communication (WOC-2003), Banff, Canada, 14-16 July, 2003.
  14. Siu, Shirley W. I.; H. M. Au. Solution for electronic ticket in mobile media. Proceedings of Macau IT Week 2002 Seminar Series, Macau, Oct 4-6 2002.
  15. Siu, Shirley W. I.; Guo, Z. S.; Fong, S.; Zhuang, Y. Extending e-ticketing service with mobile transactions. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002.
  16. Fong, S.; Siu, Shirley W. I.; Sun, A., WebSpy: Retrieving web contents for e-business intelligence. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002.
  17. Guo, Z. S.; Siu, Shirley W. I.; Wong, C. T. Full-scale online event ticketing system – the design and implementation. Proceeding of the 13th Chinese Process Control Conference, Macau and ZhuHai, China, Jul 29-Aug 2, 2002.
  18. Siu, Shirley W. I.; Guo, Z. S. Application of electronic ticket to online trading with smart card technology. Proceedings of the 6th INFORMS Conference on Information Systems and Technology (CIST-2001), Miami Beach, Florida, U.S., Nov.3-4 2001, pp.222-239.
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