Site menu:

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). 






2017

Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations 
Pratiti Bhadra and Shirley W. I. Siu* 
(submitted)
www | pdf

distrAMP: Sequence-based Prediction of Antimicrobial Peptides Using Distribution Patterns of Amino Acid Properties and Random Forest Algorithm
Pratiti Bhadra, Jielu Yu, Jinyan Li, Simon Fong and Shirley W. I. Siu* 
(submitted)
www | pdf

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*
(submitted)
www | pdf


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 doi:10.1007/s10822-017-0047-0
www | pdf


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
www | pdf


2016

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
www | pdf

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)
www | pdf

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.
www | pdf

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.
www | pdf

2015

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
www | pdf

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.
www | pdf

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.
www | pdf

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

2013

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.

www | pdf

2012

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.

www | pdf

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. 
www | pdf

2010

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.
www
 | pdf

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

2009

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
www | pdf

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.
www | pdf

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 

2008

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.
www | pdf

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.
www | pdf

2007

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.
www | pdf

2006

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

2004

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.
www | pdf

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