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Studying phase transition temperature of pentadecane using MD simulations

PUBLICATIONS

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). 






2018

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 activies in zebrafish

Archives of Toxicology, https://doi.org/10.1007/s00204-018-2334-5. (IF 5.728)
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Hang Lin and Shirley W. I. Siu*
A Hybrid Cuckoo Search and Differential Evolution Approach to Protein-Ligand Docking

International Journal of Molecular Sciences, 19 (10), 3181. (IF 3.687)
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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, 10, 238, 2018.
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, 9, 1382, 2018. (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, 10 (5), 168, 2018. (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, 8: 1697, 2018. (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, 17(2):891-902, 2018. (IF 3.950)
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2017

Pratiti Bhadra and Shirley W. I. Siu*
Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations 
Journal of Physical Chemistry C, 121, 47, 26340-26349, 2017.(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, 31: 855-865, 2017. (IF 2.356)
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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, 12: 486-489, 2017. (IF 0.841)
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2016

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

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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, 32, 2537-2538, 2016. (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, 25, 1564-1573, 2016. (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

2015

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
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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), 13 (3), 1541007, 2015.
(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, Article ID 193049, 2015. (IF 2.207)
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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 5, 1093-1098, 2015. (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 5, 1108-1115, 2015. (IF 0.549)
www | pdf

2013

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

2012

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 32, 15983-15997, 2012.
(IF 5.970)
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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 8, 1459-1470, 2012. (IF 5.399)
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2010

Ling Wang, Shirley W. I. Siu, Wei Gu, and Volkhard Helms
Downhill Binding Energy Surface of the Barnase-Barstar Complex.
Biopolymers 93, 977–985, 2010. (IF 1.990)
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 | 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 16, 1625-1637, 2010. (IF 1.507)
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2009

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
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Shirley W.I. Siu and Rainer A. Böckmann
Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin
Journal of Physical Chemistry B 113: 3195-3202, 2009. (IF 3.146)
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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 113: 7235-7243, 2009. (IF 2.836)
www | pdf 

2008

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 382: 978-986, 2008. (IF 4.894)
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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 128: 125103, 2008. (IF 2.843)
selected for April issue of Virtual Journal of Biological Physics Research.
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2007

Shirley W. I. Siu and Rainer A. Böckmann
Electric Field Effects on Membranes: Gramicidin A as a Test Ground
Journal of Structural Biology 157: 545-556, 2007. (IF 3.433)
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2006

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 22 (14): e16-e24, 2006. (IF 5.481)
www | pdf

2004

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.