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Studying phase transition temperature of pentadecane using MD simulations


Reparameterization of the OPLS-AA force field for hydrocarbons

By simulating from a half-gel starting structure, we are able to determine accurately the phase transition temperature of pentadecanes with the optimized L-OPLS parameters (Siu et al., JCTC 2012). 


Faraz Shaikh, Hio Kuan Tai, Nirali Desai, Shi, and Shirley W. I. Siu*
LigTMap: Ligand and Structure-based Target Identification and Activity Prediction for Small Molcules

Journal xxx 2020, submitted. (IF --)
www | pdf | LigTMap server

Kin Meng Wong, Hio Kuan Tai, and Shirley W. I. Siu*
Evaluation of Grey Wolf Optimization Algorithm on Rigid and Flexible Receptor Docking

Journal xxx 2020, submitted. (IF --)
www | pdf | ChemRxiv

Rui Ma, Zhili Ren, Bin Li, Shirley W. I. Siu, Guokai Chen, Hang Fai Kwok*
Novel venom-based peptides (P13 and its derivative-M6) to maintain self-renewal of human embryonic stem cells by activating FGF and TGF
β signaling pathways
Stem Cell Research & Therapy 2020, 11, 243. (IF 4.627)
www | pdf | suppl

Jielu Yan, Pratiti Bhadra, Ang Li, Pooja Sethiya, Longguang Qin, Hio Kuan Tai, Koon Ho Wong, and Shirley W. I. Siu*
Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning

Molecular Therapy - Nucleic Acid 2020, In press. (IF 5.919)
www | pdf | AxPEP server

Jiarui Chen and Shirley W. I. Siu*
Machine Learning Approaches for Quality Assessment of Protein Structures

Biomolecules 2020, 10(4), 626. (IF 4.694)
www | pdf

Jiarui Chen, Hong-Hin Cheong, and Shirley W. I. Siu*
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
www | pdf

Meng Chi Ao and Shirley W. I. Siu*
Evaluating Variants of Firefly Algorithm for Ligand Pose Prediction in Protein-Ligand Docking Program
Proceedings of the 12th International Conference on Bioinformatics and Biomedical Technology (ICBBT2020), accepted. 
www | pdf

Lu Gao and Shirley W. I. Siu*
Study of Data Imbalanced Problem in Protein-Peptide Binding Prediction
Proceedings of the 12th International Conference on Bioinformatics and Biomedical Technology (ICBBT2020), accepted. 
www | pdf


Rui Ma, Sin Wa Wong, Lilin Ge, Chris Shaw, Shirley W. I. Siu, 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. (IF 5.71)
www | pdf | suppl

Pratiti Bhadra and Shirley W. I. Siu*
Refined Empirical Force Field to Model Protein-Self-Assembled Monolayer Interactions Based on AMBER14 and GAFF

Langmuir 2019, 35 (29), 9622-9633. (IF 3.789)
www | pdf

Qiwen Liao, Guiyi Gong, Terence C. W. Poon, Irene L. Ang, Kate M. K. Lei, Shirley W. I. Siu, Clarence Tsun Ting Wong, Gandhi Rádis‑Baptista*, Simon Ming‑Yuen Lee*
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. (IF 5.741)

Faraz Shaikh+, Yuguang Zhao+, Luis Alvarez, Maria Iliopoulou, Christopher Thomas Lohans, Christopher J. Schofield, Sergi Padilla-Parra, Shirley W. I. Siu, Elizabeth Fry, Jingshan Ren, and David I. Stuart*
Structure-Based In Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library

Journal of Medicinal Chemistry 2019, 62, 2928-2937. (IF 6.253)
+equal contribution
www | pdf


Hio Kuan Tai, Siti Azma Jusoh, Shirley W. I. Siu*
Chaos-Embedded Particle Swarm Optimization Approach for Protein-Ligand Docking and Virtual Screening

Journal of Cheminformatics 2018, 10, 62. (IF 3.893)
www | pdf

Qiwen Liao, Shengnan Li, Shirley W. I. Siu, Jean‑Étienne R. L. Morlighem, Clarence Tsun Ting Wong,
Xiufen Wang, Gandhi Rádis‑Baptista*, Simon Ming‑Yuen Lee*
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. (IF 5.728)
www | pdf

Hang Lin and Shirley W. I. Siu*
A Hybrid Cuckoo Search and Differential Evolution Approach to Protein-Ligand Docking

International Journal of Molecular Sciences 2018, 19 (10), 3181. (IF 3.687)
www | pdf 

Qiwen Liao, Guiyi Gong, Shirley Weng In Siu, Clarence Tsun Ting Wong, Yu Chung Tse, Gandhi Rádis-Baptista*, Simon Ming Yuen Lee*
A Novel ShK-like Toxic Peptide from the Transcriptome of the Cnidarian Palythoa Caribaeorum displays Neuroprotection and Cardioprotection in Zebrafish
(IF 3.273)
Toxins 2018, 10, 238.
www | pdf | supplementary material

Faraz Shaikh+, Jiang He+, Pratiti, Bhadra, Xin Chen*, Shirley W. I. Siu*
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. (IF 5.511)
+equal contribution
www | pdf | supplementary material

Kairong Duan*, Simon Fong*, Shirley W. I. Siu, Wei Song, Steven Sheng-Uei Guan 
Adaptive Incremental genetic algorithm for task scheduling in cloud
Symmetry 2018, 10 (5), 168. (IF 1.457)
www | pdf 

Pratiti Bhadra, Jielu Yan, Jinyan Li, Simon Fong and Shirley W. I. Siu*
AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest
Scientific Reports 2018, 8: 1697. (IF 4.122)
www | pdf | supplementary material

Qiwen Liao, Shengnan Li, Shirley Weng In Siu, Binrui Yang, Chen Huang, Judy Yuet-Wa Chan, Jean-Étienne Morlighem, Clarence Tsun Ting Wong, Gandhi Radis-Baptista, and Simon Ming-Yuen Lee
Novel Kunitz-like peptides discovered in the zoanthid Palythoa caribaeorum through transcriptome sequencing   
Journal of Proteome Research 2018, 17(2):891-902. (IF 3.950)
www | pdf


Pratiti Bhadra and Shirley W. I. Siu*
Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations 
Journal of Physical Chemistry C 2017, 121, 47, 26340-26349.(IF 4.484)
www | pdf | supporting info 

Han Cao, Marcus C. K. Ng, Siti Azma Jusoh, Hio Kuan Tai and Shirley W. I. Siu*
TMDIM: An Improved Algorithm for the Structure Prediction of Transmembrane Domains of Bitopic Dimers
Journal of Computer-Aided Molecular Design 2017, 31: 855-865, 2017. (IF 2.356)
www | pdf

Hoi Kei Chan, Pui In Mak, Shirley W. I. Siu*
Exploring the Behavior of Water Nanodroplet on a Coplanar Electrowetting-on-Dielectric: A Molecular Dynamics Approach
IET Micro & Nano Letters 2017, 12: 486-489, 2017. (IF 0.841)
www | pdf


Wendy W. T. Lam and Shirley W. I. Siu*
PyMOL mControl: Manipulating Molecular Visualization with Mobile Devices  
Biochemistry and Molecular Biology Education 2016, doi:10.1002/bmb.20987. (IF 1.036)
www | pdf 

Jinyan Li, Simon Fong, Shirley W. I. Siu*, Sabah Mohammed, Jian Fiaidhi, and Kelvin K. L. Wong 
Improving Classification of Protein Binders for Virtual Drug Screening by Novel Swarm-Based Feature Selection Techniques
Computerized Medical Imaging and Graphics 

www | pdf

Jimmy C. F. Ngai, Pui-In Mak and Shirley W. I. Siu*
ProtPOS: A Python Package for the Prediction of Protein Preferred Orientation on a Surface
Bioinformatics 2016, 32, 2537-2538. (IF 5.481)
www | pdf | supporting info

Identification of Novel Natural Compound Inhibitors for Human Complement Component 5a Receptor by Homology Modeling and Virtual Screening
Faraz Shaikh and Shirley W. I. Siu*
Medicinal Chemistry Research 2016, 25, 1564-1573. (IF 1.607)
www | pdf

Hoi Kuan Tai, Hang Lin, and Shirley W. I. Siu*
Improving the Efficiency of PSOVina for Protein-Ligand Docking by Two-Stage Local Search
The 2016 IEEE Congress on Evolutionary Computation (CEC2016), To appear in conference proceeding
Vancouver, Canada, July 24-29, 2016.
www | pdf


Jimmy C. F. Ngai, Pui-In Mak, and Shirley W. I. Siu*
Predicting Favorable Protein Docking Poses on a Solid Surface by Particle Swarm Optimization  
Proceedings of the 2015 IEEE Congress on Evolutionary Computation (CEC2015)
, 2745-2752
Sendai, Japan, May 25-28, 2015
www | pdf

Marcus C. K. Ng, Simon Fong, and Shirley W. I. Siu*
PSOVina: The Hybrid Particle Swarm Optimization Algorithm for Protein-Ligand Docking  
Journal of Bioinformatics and Computational Biology (JBCB) 2015, 13 (3), 1541007.
(IF 0.991)
www | pdf | software

Runmiao Wang, Hui Zhou, Shirley W. I. Siu, Yong Gan, Yitao Wang and Defang Ouyang  
Comparison of Three Molecular Simulation Approaches for Cyclodextrin-Ibuprofen Complexation  
Journal of Nanomaterials 2015, Article ID 193049. (IF 2.207)
www | pdf

Simon Fong, Justin Liang, Shirley W. I. Siu, and Jonathan H. Chan
Efficient Variation-Based Feature Selection for Medical Data Classification  
Journal of Medical Imaging and Health Informatics 2015, 5, 1093-1098. (IF 0.549)
www | pdf

Simon Fong, Shirley W. I. Siu, Suzy Zhou, Jonathan H. Chan, Sabah Mohammed, and Jinan Fiaidhi  
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. (IF 0.549)
www | pdf


Shirley W. I. Siu, Thomas K. F. Wong, and Simon Fong
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.

www | pdf


Maria Borisovska, Yvonne N. Schwarz, Daniele Narzi, Shirley W. I. Siu, Jaideep Kesavan, Ralf Mohrmann, Rainer A. Böckmann and Dieter Bruns
Membrane-Proximal Tryptophanes of Synaptobrevin II Stabilize Priming of Secretory Vesicles 
Journal of Neuroscience 2012, 32, 15983-15997.
(IF 5.970)
www | pdf

Shirley W. I. Siu, Kristyna Pluhackova, Rainer A. Böckmann
Optimization of the  OPLS-AA Force Field for Long Hydrocarbons

Journal of Chemical Theory and Computation 2012, 8, 1459-1470. (IF 5.399)
www | pdf


Ling Wang, Shirley W. I. Siu, Wei Gu, and Volkhard Helms
Downhill Binding Energy Surface of the Barnase-Barstar Complex.
Biopolymers 2010, 93, 977–985. (IF 1.990)
 | pdf

Siti Azma Jusoh, Christoph Welsch, Shirley W.I. Siu, Rainer A. Böckmann, Volkhard Helms
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. (IF 1.507)
www | pdf


Rui Wang, Shirley W.I. Siu, Rainer A. Böckmann
Fine-Grained Protein Mutation Extraction from Biological Literature.

Proceedings of International Conference on Electronic Computer Technology 2009, 401-405, Macau, China, IEEE Computer Society, 2009.2
www | pdf

Shirley W.I. Siu and Rainer A. Böckmann
Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin
Journal of Physical Chemistry B 2009, 113: 3195-3202. (IF 3.146)
www | pdf

R. Vacha, Shirley W. I. Siu, M. Petrov, R.A. Böckmann, J. Barucha-Kraszewska, P. Jurkiewicz, M. Hof, M. L. Berkowitz, P. Jungwirth
Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane
Journal of Physical Chemistry A 2009, 113: 7235-7243. (IF 2.836)
www | pdf 


Daniele Narzi, Shirley W. I. Siu, Christian U. Stirnimann, John P.A. Grimshaw, Rudi Glockshuber, Guido Capitani, Rainer A. Böckmann
Evidence for Proton Shuffling in a Thioredoxin-like Protein During Catalysis
Journal of Molecular Biology 2008, 382: 978-986. (IF 4.894)
www | pdf

Shirley W. I. Siu, Robert Vacha, Pavel Jungwirth, Rainer A. Böckmann
Biomolecular Simulations of Membranes: Physical Properties from Different Force Fields
Journal of Chemical Physics 2008, 128: 125103. (IF 2.843)
selected for April issue of Virtual Journal of Biological Physics Research.
www | pdf


Shirley W. I. Siu and Rainer A. Böckmann
Electric Field Effects on Membranes: Gramicidin A as a Test Ground
Journal of Structural Biology 2007, 157: 545-556. (IF 3.433)
www | pdf


Iris Antes, Shirley W. I. Siu and Thomas Lengauer
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. (IF 5.481)
www | pdf


Simon Fong and Shirley W. I. Siu
An Integrative Framework of Predictive Mining Methods for Medical Prognosis

Proceedings of IASTED the 2nd International Conference on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 16-18 February 2004.
www | pdf

See my department's official homepage for the complete list of publications before 2004.