Shirley Siu

Official Title: Research Coordinator for the Institute of Science and Environment | Associate Research Professor

Short Bio

Shirley Weng In Siu received her PhD in Natural Sciences from Saarland University in Germany in 2010. Between 2012 and 2021, she was Assistant Professor in the Department of Computer and Information Sciences at the University of Macau and the principal investigator (PI) of Computational Biology and Bioinformatics Laboratory (CBBio). Since September 2021, she has been an Associate Research Professor at the University of Saint Joseph. Her research team focuses on computational drug design, biomolecular simulation, cheminformatics and machine learning. They are pioneering the application of swarm intelligence, machine learning, and deep learning to solve problems in protein ligand docking, drug target identification, and prediction of biological activity and toxicity. They are interested in finding new chemical and biological agents with medicinal potential. To date, their computational methods PSOVina, AmPEP, GWOVina, BESTox, LigTMap, etc. have been used and regularly cited (https://app.cbbio.online/). Shirley has great interest in the biophysics of proteins, membranes and polymers. Using molecular dynamics simulations, she has studied the conformational dynamics and mode of action of peptides from nature that are antimicrobial, anticancer, and neurotoxic. She has identified novel antimicrobial and anticancer peptides from the genomes of microbes. She has been involved in the development of membrane lipid force fields and more recently in the modelling of self-assembling monolayers on biochips.

Shirley is the author/co-author of more than 60 peer-reviewed journal and conference papers. According to the statistics of Google Scholar, her papers are cited more than 1,400 times and the author's H-index is 16. She is a member of the society Asian Association for Computer-Aided Drug Design (CADD-Asia) and Macau Computational Pharmacy Society. She has also been a member of the program committee of international bioinformatics and biomedical conferences.

Links: Google scholar, ISE's homepage, Computational tools for drug discovery (AxPEP, AcPEP, LigTMap, BESTox, etc.)

Publications

Please refer to the ISE page for the complete list of publications.

Selected Journal Papers

2022

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.
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, 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.

2021

Chen, J.; Cheong, H.H. and Siu, Shirley W. I.* xDeep-AcPEP: Deep Learning Method for Anticancer Peptide Activity Prediction Based on Convolutional Neural Network and Multitask Learning. Journal of Chemical Information and Modeling 2021, 61, 8, 3789-3803.
Shaikh, F.; Tai, H. K.; Desai, N. and Siu, Shirley W. I.* LigTMap: Ligand and structure-based target identification and activity prediction for small molecules. Journal of Cheminformatics 2021, 13: 44.
Bhadra, P. and Siu, Shirley W. I.* Effect of concentration, chain length, hydrophobicity, and an external electric fields on the growth of mixed alkanethiol self-assembled monolayers: A molecular dynamics study. Langmuir 2021, 37 (5): 1913–1924.

2020

Wong, K. M.; Tai, H. K. and Siu, Shirley W. I.* GWOVina: A grey wolf optimization approach for rigid and flexible receptor docking. Chemical Biology & Drug Design 2020, 00: 1-14.
Yan, J.; Bhadra, P.; Li, A.; Sethiya, P.; Qin, L.; Tai, H. K.; Wong, K. H.; and Siu, Shirley W. I.* Deep-AmPEP30: Improve short antimicrobial peptides prediction with deep learning. Molecular Therapy - Nucleic Acid 2020, 20, 882-894. JCR-Q1
Chen, J. and Siu, Shirley W. I.* Machine learning approaches for quality assessment of protein structures. Biomolecules 2020, 10(4), 626. JCR-Q1
Ma, R.; Wong, S. W.; Ge, L.; Shaw, C.; Shirley W. I. Siu and Hang Fai Kwok.* In vitro & Molecular dynamic simulation study to explore physicochemical parameters for antibacterial peptide to become potent anticancer peptide. Molecular Therapy - Oncolytics 2020, 16, 7-19. JCR-Q1

2019

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
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

2018

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
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
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

2017

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.

2016

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

2015

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

2012

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

2009

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

2008

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

2007

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

2006

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

Selected Conference Papers

2020

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
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.
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.

2016

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.

2015

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.

2013

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.

2009

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.