CWU Computational Chemistry Research Group

People

Computer Science Department

Razvan Andonie, Ph.D.

Chemistry Department

Levente Fabry-Asztalos, Ph.D.

CWU Alumni

Christopher B. Abdul-Wahid (graduated 2009); presently, a PhD student (University of Notre Dame)

Grant Barker (graduated 2009); presently, a PhD student (University of Washington, Seattle)

Sarah Abdul-Wahid, M.S. (graduated 2006)

Catharine J. Collar, M.S. (graduated 2006, PhD now)

Nicholas Salim (graduated 2006)

Heather N. Biles (graduated 2006)

Lukas Magill (graduated 2008) 

International Collaborators

Istvan Lorentz, PhD student of R. Andonie. Transilvania University, Romania

Bogdan Crivat, PhD student of R. Andonie. Transilvania University, Romania, PhD 2011, presently VP of Predixion Software, USA.

Lucian Sasu, PhD student of R. Andonie, Transilvania University, Romania, PhD 2006, presently with Transilvania University and Siemens, Romania.

Our collaborative research involves modern drug discovery, the design, synthesis, and evaluation of potential enzyme inhibitory chemical compounds. Computational Intelligence and Computer Aided Molecular Modeling represent essential components of this endeavor. We are using Sybyl molecular modeling in conjunction with neural-networks - fuzzy logic - genetic algorithms techniques to design de novo structures which can become lead compounds for further drug development, and possibly future therapeutic agents.

Publications

1.     Andonie R., Fabry-Asztalos L., Sasu, L. Bayesian ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors using A Small Molecular Dataset, Proceedings of the IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB 2014), May 21-24, 2014, Honolulu, Hawaii, USA.

2.     Lorentz I., Andonie R., Fabry-Asztalos L. Solving Molecular Distance Geometry Problems in OpenCL, Proceedings of the 13th International Conference on Optimization of Electrical and Electronic Equipment, (OPTIM'2012), Brasov, Romania, May 24-26, 2012, 1421-1428.

3.     Fabry-Asztalos, L., Lorentz I., Andonie, R. Molecular Distance Geometry Optimization using Geometric Build-up and Evolutionary Techniques on GPU, Proceedings of the IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB 2012), May 9-12, 2012, San Diego, USA, 321-328.

4.     Razvan Andonie, Levente Fabry-Asztalos, C. Badi‘ Abdul-Wahid, Sarah Abdul-Wahid, Grant Barker, Lukas Magill. Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors using A Small Molecular Dataset, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 2011, 80-93.

5.     Andonie R., Fabry‑Asztalos L., Crivat B., Abdul‑Wahid S., Abdul‑Wahid B. Fuzzy ARTMAP Rule Extraction in Computational Chemistry, Proceedings of the IEEE International Joint Conference on Neural Networks (IJCNN 2009), Atlanta, June 14-19, 2009, 157-163, Best Poster Award Runner-up.

6.     Fabry-Asztalos, L., Andonie, R., Collar, C., Abdul-Wahid, S., Salim, N. A Genetic Algorithm Optimized Fuzzy Neural Network Analysis of the Affinity of Inhibitors for HIV-1 Protease, Bioorganic & Medicinal Chemistry, 16, 2008, 2903-2911.

7.     Andonie R., Fabry‑Asztalos L., Magill L., Abdul‑Wahid S. A New Fuzzy ARTMAP Approach for Predicting Biological Activity of Potential HIV‑1 Protease Inhibitors, Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), San Jose, CA, Nov 2-4, 2007, IEEE Computer Society Press, ISBN 0-7695-3031-1, 56-61.

8.     Andonie, R., Fabry-Asztalos, L., Abdul-Wahid, S., Collar, C., Salim, N. An Integrated Soft Computing Approach for Predicting Biological Activity of Potential HIV-1 Protease Inhibitors, Proceedings of the IEEE International Conference on Neural Networks (IJCNN 2006), Vancouver, BC, Canada, July 16-21, 2006, 7495-7502, Best Session Presentation Award.

9.     Andonie, R., Fabry-Asztalos, L., Collar, C., Abdul-Wahid, S., Salim, N. Neuro-fuzzy Prediction of Biological Activity and Rule Extraction for HIV-1 Protease Inhibitors, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'05), San Diego, November 14-15, 2005, 113-120.

Presentations

1.     Levente Fabry-Asztalos, Razvan Andonie. Fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease, Oral presentation at the 243rd American Chemical Society National Meeting, San Diego, CA, March 27, 2012.

  1. Kristoffer Hepler, Forrest Williamson, Zachary Haberman, Razvan Andonie, Levente Fabry-Asztalos. Bee Colony Optimization of Protein Folding, Symposium on University Research and Creative Expression (SOURCE 2011), Ellensburg, May 19, 2011.
  2. Forrest Williamson,  Kristoffer Hepler, Zachary Haberman, Levente Fabry-Asztalos, Razvan Andonie. Analysis of Cathepsin-D Inhibitory Compounds by Computational Intelligence Methods, Symposium on University Research and Creative Expression (SOURCE 2011), Ellensburg, May 19, 2011.

4.     BadiAdbul-Wahid, Grant I. Barker, Sarah Abdul-Wahid, Luke Magill, Catharine Collar, Nicholas  Salim, Razvan Andonie*, Levente Fabry-Asztalos*. Using Computational Intelligence as Predictive Tool for Biological Activities of Drug Candidates Targeted Towards Therapeutically Important Enzymes for Rapid Screening, Posters on the Hill, Council on Undergraduate Research, Capitol Hill, Washington DC, May 5th, 2009. The posters are presented to the members of Congress.

5.     Badi‘ Abdul-Wahid, Razvan Andonie, Levente Fabry-Asztalos, Bogdan Crivat, Sarah Abdul-Wahid. Fuzzy ARTMAP Rule Extraction in Computational Chemistry, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

6.     Badi' Abdul-Wahid, Gene Roseberry, Zacharias Thompson, Branden Lopez, Levente Fabry-Asztalos, Razvan Andonie. Applications of Graph Matching for Chemical Structures, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

7.     Badi' Abdul-Wahid, Grant Barker, Razvan Andonie, Levente Fabry-Asztalos. Predictive Software as a Rapid Screening Tool for Potential Drug Candidates, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

8.     Badi' Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. Prediction of Biological Efficacy for Potential Plasmodium Falciparum Plasmepsin IV Inhibitors, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

9.     BadiAdbul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. Prediction of Biological Efficacy for Potential Plasmodium Falciparum Plasmepsin IV Inhibitors,  Seattle Parasitology Conference, Seattle Biomedical Research Institute, May 14-15, 2009.

10.  Grant I. Barker, Razvan Andonie, Levente Fabry-Asztalos. Computer modeling and neural networks used in the design of novel HIV-1 protease inhibitors for the therapeutic treatment of HIV/AIDS, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008.

11.  Badi’Adbul-Wahid, Razvan Andonie, Levente Fabry-Asztalos. Prediction of novel inhibitors targeting P. Falciparum Plasmepsin IV, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008.

12.  Badi’Adbul-Wahid, Grant I. Barker, Razvan Andonie, Levente Fabry-Asztalos. Ordered Fuzzy ARTMAP for predicting HIV-1 protease inhibitor activity, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008, Outstanding Oral Presentation Award.

13.  BadiAdbul-Wahid, Grant Barker, Levente Fabry-Asztalos, Razvan Andonie, Ordered Fuzzy ARTMAP for Predicting HIV-1 Protease Inhibitors, 2008 American Chemical Society – Puget Sound Section Undergraduate Research Symposium, The Evergreen State College, Olympia, WA, April 26th, 2008.

14.  Lukas Magill, Razvan Andonie, Levente Fabry-Asztalos, Genetic Algorithm Optimized Fuzzy ARTMAP with Relevancies for HIV-1 Protease Prediction, Symposium on University Research and Creative Expression (SOURCE 2007), Ellensburg, May 17, 2007.

15.  BadiAdbul-Wahid, Levente Fabry-Asztalos, Sarah Abdul-Wahid, Razvan Andonie, Dimensional abstraction: Generating novel potential inhibitors of Malarial Plasmepsin IV using computational methodologies, Symposium on University Research and Creative Expression (SOURCE 2007), Ellensburg, May 17, 2007.

16.  BadiAdbul-Wahid, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. In Silico Study of Plasmodium Falciparum Proteases Plasmepsin II and IV: Prediction of Biological Activity of Newly Designed Inhibitors, the 233th American Chemical Society National Meeting, Chicago, IL, March 25-29, 2007.

17.  Andonie, R. Predicting Biological Activity of Potential HIV-1 Protease Inhibitors – A Computational Intelligence Approach, November 10th, 2006, Old Dominium University, Norfolk, VA, invited tutorial presentation.

18.  Nicholas Salim, Catharine J. Collar, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie.  Fuzzy-neural network predictions of IC50 values for potential HIV-1 protease inhibitors, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006.

19.  Sarah Abdul-Wahid, Catharine J. Collar, Nicholas Salim, Razvan Andonie, Levente Fabry-Asztalos.  An integrated computational intelligence approach for predicting biological activity of potential HIV-1 protease inhibitors, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006.

20.  Nicholas Salim, Sarah Abdul-Wahid, Catharine J. Collar, Levente Fabry-Asztalos, Razvan Andonie. Application of a Fuzzy-Neural Network to Predict IC50 Values for Potential HIV-1 Protease Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2006.

21.  Levente Fabry-Asztalos, Razvan Andonie, Catharine J. Collar, Sarah Abdul-Wahid, Nicholas Salim. Neuro-Fuzzy Prediction of Biological Activity and IF/THEN Rule Extraction for HIV-1 Protease Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2006.

22.  Nicholas Salim, Catharine J. Collar, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Rǎzvan Andonie. Application of fuzzy neural networks to predict IC50 values of novel HIV-1 protease inhibitors, oral presentation, the 14th Regional Murdock Conference on Undergraduate Research, Nampa, ID, November 12, 2005.

23.  Catharine J. Collar and Levente Fabry-Asztalos. Modeling Bioactivity for Aspartic Protease Inhibitors Using Bioavailability and Physicochemical Molecular Descriptors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2005.

24.  Heather Biles, Michael Ellis, Catharine J. Collar, Levente Fabry-Asztalos. Analyzing Force Field and Charge Conditions to Enhance Biological Activity Predictions of Cathepsin D Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2005.

25.  Sarah Abdul-Wahid, Catharine J. Collar, Nicholas Salim, Razvan Andonie, Levente Fabry-Asztalos. Explicit Knowledge Extraction from Properties of Chemical Structures, poster presentation, Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

26.  Catharine Collar, Sarah Abdul-Wahid, Nicholas Salim, Levente Fabry-Asztalos, Razvan Andonie. Neuro-Fuzzy and Multiple Regression IC50 Prediction of HIV-1 Protease Inhibitors, oral presentation,  Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

27.  Catharine Collar, Levente Fabry-Asztalos. Predicting Biological Activity of HIV-1 Protease Inhibitors Using Multi-Variable Molecular Mathematical Modeling, oral presentation, Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

28.  Sarah Abdul-Wahid, Nicholas Salim, Catharine J. Collar, Razvan Andonie, Levente Fabry-Asztalos. Predicting Biological Affinity of HIV-1 Protease Inhibitors Using A Neuro-Fuzzy Network, poster presentation, American Chemical Society Puget Sound Section Undergraduate Research Symposium, Seattle, WA, April 23, 2005.

29.  Heather N. Biles, Catharine J. Collar, Levente Fabry-Asztalos. Molecular Modeling of Cathepsin-D Inhibitors; A Comparative Study with Pepstatin, poster presentation, the 14th Regional Murdock Conference on Undergraduate Research, Nampa, ID, November 19, 2004.