25. Raed Khashan. SCORPIONS: A Scoring Function for Computationally Generated Protein Folds using 3D Structural Motifs derived by Mining Internal Residues in Native Protein Structures. In preparation.
24. Raed Khashan, and Grace Brannigan. Estimating Binding Affinities of GABAa Neuromodulators: Using Free Energy Methods in Combination with Large Scale Molecular Dynamics Simulations. In preparation.
23. Raed Khashan and Ingo Muegge. mbiPMF: Accounting for Multi-body Interactions in the Knowledge-based PMF Scoring Function for Protein-Ligand Interactions. In preparation.
22. Raed Khashan. ChemIsosteres: Structure-based Bioisosteres Sharing Related Binding Pockets with Similar Geometric & Chemical Features. In preparation.
21. Raed Khashan and Faruk Khan. Chapter 35: Drug Discovery and Development. In: Medicinal Chemistry for Pharmacy Students. Edited by: M. O. Faruk Khan. In preparation.
20. Saousen Diaf, Amnah Alalmaei, Sanzana Rivu and Raed Khashan. Implications of Molecular and Structural Mechanism of Insulin Receptor on Receptor Activation and Drug Design. Membranes (Under Review).
19. Amnah Alalmaei, Saousen Diaf, and Raed Khashan. Molecular and Structural Mechanism of DNA Targeting by a Transposon-encoded Type I-F CRISPR/Cas. The CRISPR Journal (Under Review).
18. Raed Khashan. Using AI Strategies to Support Fragment-based De Novo Drug Design (FragDeNovo) using Pocket Similarity Search of Native Protein-Ligand Complexes. Molecular Informatics (Under Review).
17. Raed Khashan. Data Mining Meets Machine Learning: Performing Fragment-based Virtual Screening (FragVScreen) using Pocket Similarity Search of Native Protein-Ligand Complexes. Journal of Chemical Information and Modeling (Under Review).
16. Raed Khashan, Alexander Tropsha, and Weifan Zheng. Data Mining Meets Machine Learning: A Novel ANN-based Multi-Body Interaction Docking Scoring Function (MBI-Score) based on Utilizing Frequent Geometric and Chemical Patterns of Interfacial Atoms in Native Protein-Ligand Complexes. Molecular Informatics, Accepted on Feb. 9, 2022. (doi: 10.1002/minf.202100248)
15. Raed Khashan. Chapter 3: Generating “Fragment-Based Virtual Library” Using Pocket Similarity Search of Ligand-Receptor Complexes. In: Fragment-Based Methods in Drug Discovery, Methods in Molecular Biology. Edited by: Anthony E. Klon. Vol. 1289, pp. 23-30, 2015.
14. Raed Khashan, Weifan Zheng, and Alexander Tropsha. The Development of Novel Chemical Fragment-Based Descriptors Using Frequent Common Subgraph Mining Approach and Their Application in QSAR Modeling. Molecular Informatics, Vol. 33, Issue 3, pp. 201-215, 2014.
13. Raed Khashan. FragVLib – A Free Program for Generating “Fragment-based Virtual Library” Using Pocket Similarity Search of Ligand-Receptor Complexes. Journal of Cheminformatics, Vol. 4, Issue 1, pp. 18, 2012.
12. Raed Khashan, Weifan Zheng, and Alexander Tropsha*. Scoring Protein Interaction Decoys using Exposed Residues (SPIDER): A Novel Multi-Body Interaction Scoring Function based on Frequent Geometric Patterns of Interfacial Residues. Proteins: Structure, Function, and Bioinformatics, Vol. 80, Issue 9, pp. 2207-2217, 2012.
11. Sarel J. Fleishman, Timothy A. Whitehead, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, et al. Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology. Journal of Molecular Biology, Vol. 414, Issue 2, pp. 289-302, 2011.
10. Raed Khashan and Weifan Zheng. FragVLib: Fragment-based virtual screening library using geometric and chemical patterns of interactions at interface of ligand-receptor complex crystal structures. Abstracts of Papers, 240th ACS National Meeting, Boston, MA, August 22-26, 2010, COMP-216.
9. Raed Khashan, Weifan Zheng, and Alexander Tropsha. GeoIsosteres: Structure-based approach to finding bioisosteres using geometric & chemical patterns of interacting atoms at receptor-ligand interfaces. Abstracts of Papers, 240th ACS National Meeting, Boston, MA, Aug 22, 2010, COMP-414.
8. Raed Khashan, Weifan Zheng, and Alexander Tropsha. Fragment based design and biophores using geometric and chemical patterns of interactions at interface of ligand-receptor complex crystal structures. Abstracts of Papers, 240th ACS National Meeting, Boston, MA, Aug 22, 2010, COMP-275.
7. Raed Khashan, Weifan Zheng, Wei Wang, and Alexander Tropsha. Development of scoring functions for protein ligand binding based on frequent geometric and chemical patterns of inter-atomic interactions at their interfaces. Abstracts of Papers, 234th ACS National Meeting, Boston, MA, August 19-23, 2007, COMP-352.
6. Raed Khashan, Weifan Zheng, Wei Wang, and Alexander Tropsha. Development of docking protocols & scoring functions using frequent geometric & chemical patterns of inter-atomic interactions at the interface of protein- ligand complexes. Abstracts of Papers, 233rd ACS National Meeting, Chicago, IL, March 25-29, 2007, COMP 191, & COMP-261.
5. Raed Khashan. Development and Application of Ligand/Structure-based Computational Drug Discovery Tools Based on Frequent Subgraph Mining of Chemical Structures. Dissertation (Ph.D. in Pharmacy) — University of North Carolina at Chapel Hill, August 2007.
4. Raed Khashan, Weifan Zheng, Jun Huan, Wei Wang, and Alexander Tropsha. Development of fragment-based chemical descriptors using novel frequent common subgraph mining approach and their application in QSAR modeling. Abstracts of Papers, 230th ACS National Meeting, Washington, DC, Aug. 28-Sept. 1, 2005, COMP-177, & COMP-337.
3. Scott Oloff, Raed Khashan, Robert Plourde, and Alex Tropsha. Develop. of valid. QSAR models of P2Y12 receptor antag. & their app. to database mining. Abs. of Papers, 227th ACS Nat. Meet., Anaheim, CA, Mar 28-Apr 1, 2004, MEDI-300.
2. Raed Khashan. Refinement and Validation of BCUT Descriptors for Computer Assisted Drug Discovery. Thesis (M.S. in Pharmacy) — University of Texas at Austin, August 2003.
1. Robert Pearlman, Raed Khashan, D. Wong, and Renzo Balducci. ProtoPlex: User-control over tautomeric & protonation state. Abstracts of Papers, 224th ACS National Meeting, Boston, MA, August 18-22, 2002, COMP- 232.
PI: Ra'ed Khashan, PhD, RPh
