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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). 

Journal

Conference



Journal Publications

    2021

  1. 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. Submitted.
  2. 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. https://doi.org/10.1021/acs.langmuir.0c03414

  3. 2020

  4. Li, Tengyue; Fong, Simon; Siu, Shirley W. I.; Yang, Xin-she; Liu, Lian-Sheng; Mohammed, Sabah. White learning methodology: A case study of cancer-related disease factors analysis in real-time PACS environment. Computer Methods and Programs in Biomedicine 2020, 197: 105724. JCR-Q1
  5. 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.
  6. Ma, R.; Ren, Z.; Li, B.; Siu, Shirley W. I.; Chen, G.; Kwok, H. F. Novel venom-based peptides (P13 and its derivative-M6) to maintain self-renewal of human embryonic stem cells by activating FGF and TGFß signaling pathways. Stem Cell Research & Therapy 2020, 11, 243. JCR-Q1
  7. 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
  8. Chen, J. and Siu, Shirley W. I.* Machine learning approaches for quality assessment of protein structures. Biomolecules 2020, 10(4), 626. JCR-Q1
  9. 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

  10. 2019

  11. 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
  12. Liao, Q.; Gong, G.; Poon, T. C. W.; Ang, I. L.; Lei, K. M. K.; Siu, Shirley W. I; Wong, C. T. T.; Rádis-Baptista, G.*; Lee, M. Y.*. 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. JCR-Q1
  13. 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

  14. 2018

  15. 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
  16. 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
  17. Liao, Q.; Li, S.; Siu, Shirley W. I.; Morlighem, J.-É. R. L.; Wong, C. T. T.; Wang, X.; Rádis-Baptista, G.*; Lee, M.-Y.*. 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 2018, 93, 189-206. JCR-Q1
  18. 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
  19. Liao, Q.; Gong, G.; Siu, Shirley W. I.; Wong, C. T. T.; Tse, Y. C.; Rádis-Baptista, G.*; Lee, M.-Y.* A novel ShK-like toxic peptide from the transcriptome of the cnidarian Palythoa caribaeorum displays neuroprotection and cardioprotection in zebrafish. Toxins 2018, 10 (6): 238. JCR-Q1
  20. Duan, K.*; Fong, S.*; Siu, Shirley W. I.; Song, W.; Guan, S. S.-U. Adaptive incremental genetic algorithm for task scheduling in cloud. Symmetry 2018 10 (5), 168.
  21. Liao, Q.; Li, S.; Siu, Shirley W. I.; Yang, B.; Huang, C.; Chan, J.; Morlighem, J.-É.; Wong, C.; Radis-Baptista, G.; Lee, M.-Y. Novel Kunitz-like peptides discovered in the zoanthid Palythoa caribaeorum through transcriptome sequencing. Journal of Proteome Research 2018, 17 (2), 891-902. JCR-Q1
  22. 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

  23. 2017

  24. 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
  25. 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.

  26. 2016

  27. 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.
  28. 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.
  29. 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.
  30. 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

  31. 2015

  32. 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
  33. Wang, R.; Zhou, H.; Siu, Shirley W. I.; Gan, Y.; Wang, Y.; Ouyang, D.* Comparison of three molecular simulation approaches for cyclodextrin-ibuprofen complexation. Journal of Nanomaterials 2015, Article ID 193049. ESI-Q1
  34. Fong, S.*; Liang, J.; Siu, Shirley W. I.; Chan, J. H. Efficient variation-based feature selection for medical data classification. Journal of Medical Imaging and Health Informatics 2015, 5, 1093-1098.
  35. Fong, S.*; Siu, Shirley W. I.; Zhou, S.; Chan, J. H.; Mohammed, S.; Fiaidhi, J. 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.

  36. 2012

  37. 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
  38. Borisovska, M.; Schwarz, Y. N.; Narzi, D.; Siu, Shirley W. I.; Kesavan, J.; Mohrmann, R.; Böckmann, R. A.; Bruns, D.* Membrane-proximal tryptophanes of synaptobrevin II stabilize priming of secretory vesicles. Journal of Neuroscience 2012, 32, 15983-15997. JCR-Q1

  39. 2010

  40. Wang, L.; Siu, Shirley W. I.; Gu, W.; Helms, V.* Downhill binding energy surface of the barnase-barstar complex. Biopolymers 2010, 93, 977–985.
  41. Jusoh, S. A.; Welsch, C.; Siu, Shirley W. I.; Böckmann, R. A.; Helms, V.* 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.

  42. 2009

  43. 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
  44. Vacha, R.; Siu, Shirley W. I.; Petrov, M.; Böckmann, R. A., Barucha-Kraszewska, J.; Jurkiewicz, P.; Hof, M.; Berkowitz, M. L.; Jungwirth, P.* Effects of alkali cations and halide anions on the DOPC lipid membrane. Journal of Physical Chemistry A 2009, 113, 7235-7243. ESI-Q1

  45. 2008

  46. Narzi, D.; Siu, Shirley W. I.; Stirnimann, C. U.; Grimshaw, J. P.A.; Glockshuber, R.; Capitani, G.; Böckmann, R. A.* Evidence for proton shuffling in a thioredoxin-like protein during catalysis. Journal of Molecular Biology 2008, 382, 978-986. JCR-Q1
  47. 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

  48. 2007

  49. 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

  50. 2006

  51. 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


Conference Publications


    2020

  1. 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
  2. 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.
  3. 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.

  4. 2016

  5. 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.

  6. 2015

  7. 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.

  8. 2013

  9. 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.

  10. 2001-2009

  11. 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.
  12. Leung, A.; Fong, S.; Siu, Shirley W. I. Smart card-based irregular access patterns detection system. IEEE International Conference on e-Technology, e-Commerce and e-Service (EEE 2004), Taipei, Taiwan, 28-31 March 2004, pp.546-553.
  13. Fong, S.; Siu, Shirley W. I. An integrative framework of predictive mining methods for medical prognosis. IASTED the 2nd International Conference on Biomedical Engineering (BioMED 2004), Innsbruck, Austria, 16-18 February 2004.
  14. Fong, S.; Siu, Shirley W. I.; Sun, A. Market watcher agent for e-commerce. IASTED the International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004.
  15. Leung, A.; Fong, S.; Siu, Shirley W. I. Smart card-based identification and access control model with real-time suspicious action detection mechanism. IASTED The International Conference on Artificial Intelligence and Applications (AIA 2004), Innsbruck, Austria, 16-18 February 2004.
  16. Siu, Shirley W. I.; Fong, S.; Guo, Z. S.; Si Tou, K. F. Context-aware for service discovery in ad hoc environment. IASTED Intl. Conf. on Wireless and Optical Communication (WOC-2003), Banff, Canada, 14-16 July, 2003.
  17. Siu, Shirley W. I.; H. M. Au. Solution for electronic ticket in mobile media. Proceedings of Macau IT Week 2002 Seminar Series, Macau, Oct 4-6 2002.
  18. Siu, Shirley W. I.; Guo, Z. S.; Fong, S.; Zhuang, Y. Extending e-ticketing service with mobile transactions. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002.
  19. Fong, S.; Siu, Shirley W. I.; Sun, A., WebSpy: Retrieving web contents for e-business intelligence. Proceedings of the 1st International Conference on Information Technology and Applications (ICITA-2002), Bathurst, Australia, Nov. 25-29, 2002.
  20. Guo, Z. S.; Siu, Shirley W. I.; Wong, C. T. Full-scale online event ticketing system - the design and implementation. Proceeding of the 13th Chinese Process Control Conference, Macau and ZhuHai, China, Jul 29-Aug 2, 2002.
  21. Siu, Shirley W. I.; Guo, Z. S. Application of electronic ticket to online trading with smart card technology. Proceedings of the 6th INFORMS Conference on Information Systems and Technology (CIST-2001), Miami Beach, Florida, U.S., Nov.3-4 2001, pp.222-239.