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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). 


TNFR2 as an emerging drug target for the treatment of cancer and autoimmune diseases: an In silico perspective on Treg-modulatory drug discovery
Faraz Shaikh+, Jiang He+, Pratiti, Bhadra, Xin Chen*, Shirley W. I. Siu*
+equal contribution
www | pdf | supplementary material

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

A Machine Learning Approach to Anticancer Peptide Prediction using Amino Acid Composition, Profile Similarity and Water-Membrane Partitioning Free Energy
Pratiti Bhadra and Shirley W. I. Siu*
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Novel Kunitz-like peptides discovered in the zoanthid Palythoa caribaeorum through transcriptome sequencing 
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 
Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.7b00686
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Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations 
Pratiti Bhadra and Shirley W. I. Siu*
Journal of Physical Chemistry C, 121, 47, 26340-26349, 2017.
www | pdf | supporting info 

TMDIM: An Improved Algorithm for the Structure Prediction of Transmembrane Domains of Bitopic Dimers
Han Cao, Marcus C. K. Ng, Siti Azma Jusoh, Hio Kuan Tai and Shirley W. I. Siu* 

J Comput Aided Mol Des, 31: 855-865, 2017
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Exploring the Behavior of Water Nanodroplet on a Coplanar Electrowetting-on-Dielectric: A Molecular Dynamics Approach
Hoi Kei Chan, Pui In Mak, Shirley W. I. Siu*
Micro & Nano Letters doi:10.1049/mnl.2016.0824
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PyMOL mControl: Manipulating Molecular Visualization with Mobile Devices  
Wendy W. T. Lam and Shirley W. I. Siu*
Biochemistry and Molecular Biology Education doi:10.1002/bmb.20987
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Improving Classification of Protein Binders for Virtual Drug Screening by Novel Swarm-Based Feature Selection Techniques
Jinyan Li, Simon Fong, Shirley W. I. Siu*, Sabah Mohammed, Jian Fiaidhi, and Kelvin K. L. Wong
Computerized Medical Imaging and Graphics (Available online 30 September 2016)
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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*
Bioinformatics, 32, 2537-2538, 2016.
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.
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Improving the Efficiency of PSOVina for Protein-Ligand Docking by Two-Stage Local Search
Hoi Kuan Tai, Hang Lin, and Shirley W. I. Siu*
The 2016 IEEE Congress on Evolutionary Computation (CEC2016), To appear in conference proceeding
Vancouver, Canada, July 24-29, 2016.
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Predicting Favorable Protein Docking Poses on a Solid Surface by Particle Swarm Optimization  
Jimmy C. F. Ngai, Pui-In Mak, and Shirley W. I. Siu*
Proceedings of the 2015 IEEE Congress on Evolutionary Computation (CEC2015)
, 2745-2752
Sendai, Japan, May 25-28, 2015
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PSOVina: The Hybrid Particle Swarm Optimization Algorithm for Protein-Ligand Docking  
Marcus C. K. Ng, Simon Fong, and Shirley W. I. Siu*
Journal of Bioinformatics and Computational Biology (JBCB), 13 (3), 1541007, 2015.

www | pdf | software

Comparison of Three Molecular Simulation Approaches for Cyclodextrin-Ibuprofen Complexation  
Runmiao Wang, Hui Zhou, Shirley W. I. Siu, Yong Gan, Yitao Wang and Defang Ouyang
Journal of Nanomaterials, Article ID 193049, 2015.
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Efficient Variation-Based Feature Selection for Medical Data Classification  
Simon Fong, Justin Liang, Shirley W. I. Siu, and Jonathan H. Chan
Journal of Medical Imaging and Health Informatics 5, 1093-1098, 2015.
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Real-Time Analysis of Vital Signs Using Incremental Data Stream Mining Techniques with a Case Study of ARDS Under ICU Treatment  
Simon Fong, Shirley W. I. Siu, Suzy Zhou, Jonathan H. Chan, Sabah Mohammed, and Jinan Fiaidhi
Journal of Medical Imaging and Health Informatics 5, 1108-1115, 2015.
www | pdf


Comparison of Cutoff Strategies for Geometrical Features in Machine Learning-based Scoring Functions  
Shirley W. I. Siu, Thomas K. F. Wong, and Simon Fong
Proceedings of the 9th International Conference on Advanced Data Mining and Applications (ADMA2013), Hangzhou, China, December 14-16, 2013, LNAI 8347, 336-347, Springer.

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

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Optimization of the  OPLS-AA Force Field for Long Hydrocarbons
Shirley W. I. Siu, Kristyna Pluhackova, Rainer A. Böckmann
 J. Chemical Theory and Computation 8, 1459-1470, 2012. 
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Downhill Binding Energy Surface of the Barnase-Barstar Complex.
Ling Wang, Shirley W. I. Siu, Wei Gu, and Volkhard Helms
Biopolymers 93, 977–985, 2010.
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Contribution of Charged and Polar Residues for the Formation of the E1-E2 Heterodimer from Hepatitis C Virus
Siti Azma Jusoh, Christoph Welsch, Shirley W.I. Siu, Rainer A. Böckmann, Volkhard Helms
J. Mol. Model. 16, 1625-1637, 2010.
www | pdf


Fine-Grained Protein Mutation Extraction from Biological Literature.
Rui Wang, Shirley W.I. Siu, Rainer A. Böckmann
Proceedings of International Conference on Electronic Computer Technology 2009, 401-405, Macau, China, IEEE Computer Society, 2009.2
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Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin
Shirley W.I. Siu and Rainer A. Böckmann
J. Phys. Chem. B 113: 3195-3202, 2009.
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Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane
R. Vacha, Shirley W. I. Siu, M. Petrov, R.A. Böckmann, J. Barucha-Kraszewska, P. Jurkiewicz, M. Hof, M. L. Berkowitz, P. Jungwirth
J. Phys. Chem. A 113: 7235-7243, 2009.
www | pdf 


Evidence for Proton Shuffling in a Thioredoxin-like Protein During Catalysis
Daniele Narzi, Shirley W. I. Siu, Christian U. Stirnimann, John P.A. Grimshaw, Rudi Glockshuber, Guido Capitani, Rainer A. Böckmann
J. Mol. Biol. 382: 978-986, 2008.
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Biomolecular Simulations of Membranes: Physical Properties from Different Force Fields
Shirley W. I. Siu, Robert Vacha, Pavel Jungwirth, Rainer A. Böckmann
J. Chem. Phys. 128: 125103, 2008.
selected for April issue of Virtual Journal of Biological Physics Research.
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Electric Field Effects on Membranes: Gramicidin A as a Test Ground
Shirley W. I. Siu and Rainer A. Böckmann
J. Struc. Biol. 157: 545-556, 2007.
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DynaPred: A Structure and Sequence Based Method for the Prediction of MHC Class I Binding Peptide Sequences and Conformations
Iris Antes, Shirley W. I. Siu and Thomas Lengauer
Bioinformatics 22 (14): e16-e24, 2006.
www | pdf


An Integrative Framework of Predictive Mining Methods for Medical Prognosis
Simon Fong and Shirley W. I. Siu
Proceedings of IASTED the 2nd International Conference on Biomedical Engineering (BioMED 2004) , Innsbruck, Austria, 16-18 February 2004.
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See my department's official homepage for the complete list of publications before 2004.