1. Reid, T-E.; Fortunak, J.; Wutoh, A.; Wang, X. S.* Ligand-based drug discovery of human tyrosine kinase inhibitors. Current Topics in Medicinal Chemistry 2014 (Invited review, accepted)

2. Xia, J.; Tilahun, E. L.; Kebede, E. H.; Reid, T-E.; Zhang, L-R.; Wang, X. S.* Comparative modeling and benchmarking data set for human histone deacetylases and sirtuin families. J. Chem. Inf. Model. 2014 (Submitted)

3. Luo, M.; Reid, T-E.; Wang, X. S.* Discovery of natural product-derived 5HT-1A receptor binders by cheminfomatics modeling of known inhibitors, high throughput screening and experimental validation. Combinatorial Chemistry and High Throughput Screening Chemoinformatics for Virtual Screening Special Issue 2014 (In press)

4. Basant, N.; Lin, X-H.; Reid, T-E.; Karla, P. K.; Wang, X. S.* Discovery of a novel HDAC2 inhibitors by a scaffold-merging hybrid query. Combinatorial Chemistry and High Throughput Screening Chemoinformatics for Virtual Screening Special Issue 2014 (In press)

5. Xia, J.; Tilahun, E. L.; Reid, T-E.; Zhang, L-R.*; Wang, X. S.* Benchmarking methods and data sets for ligand enrichment assessment in virtual screening. Methods 2015, 71, 146157. (Invited article)

6. Kufareva, I; Katritch, V.; ...; Xia, J.; Hsieh, J-H.; Zhang, L-R.; Wang, X. S.; ; Stevens, R. C.*; Abagyan, R.* Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges. Structure 2014 (Accepted)

7. Nagarwal, R.C.; Ako-Adounvo, A-M; Boddu, S. H.; Wang, X. S.; Karla, P. K.* Recent patents on ophthalmic nanoformulations and therapeutic implications. Recent Patents on Drug Delivery & Formulation 2014, 8, 193-201.

8. Xia, J.; Jin, H-W.; Liu, Z-M.; Zhang, L-R.*; Wang, X. S.* An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs. J. Chem. Inf. Model. 2014, 54, 1433-1450. (Most read articles)

9. Luo, M.; Wang, X. S.*; Roth, B. L.; Golbraikh, A.; Tropsha, A.* Application of Quantitative Structure-Activity Relationship models of 5-HT1A receptor binding to virtual screening identifies novel and potent 5-HT1A ligands. J. Chem. Inf. Model. 2014, 54, 634647.

10. Reid, T-E.; Kumar, K.; Wang, X. S.* Predictive in silico studies of human 5-hydroxytryptamine receptor subtype 2B (5-HT2B) and valvular heart disease. Current Topics in Medicinal Chemistry 2013, 13, 1353-1362. (Invited review)

11. Lin, X.; Huang, X-P.; Peng, S.; Wang, Y.; Wang, S. X.; Roth, B. L.; Huang, N.* Life beyond kinases: Structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors. J. Med. Chem. 2012, 55, 5749-5759.

12. Tang, H.; Wang, X. S.*; Hsieh, J-H.; Tropsha, A.* Do crystal structures obviate the need for theoretical models of GPCRs for structure based virtual screening. Proteins: Structure, Function, and Bioinformatics 2012, 80, 1503-1521.

13. Hsieh, J-H.; Yin, S-Y.; Wang, X. S.; Liu, S-B.; Dokholyan, N. V.*; Tropsha, A.* Cheminformatics meets molecular mechanics: A combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening. J. Chem. Inf. Model. 2012, 52, 16-28.

14. Carroll, M. J.; Gromova, A. V.; Miller, K. R.; Tang, H.; Wang, X. S.; Tripathy, A.; Singleton, S. F.; Collins, E. J.; Lee, A. L.* Direct detection of structurally resolved dynamics in a multi-conformation receptor-ligand complex. J. Am. Chem. Soc. 2011, 133, 6422-6428.

15. Wang, X. S.; Roitberg, A. E.; Richards, N. G. J.* Computational studies of ammonia channel function in glutamine 5-phosphoribosylpyrophosphate amidotransferase. Biochemistry 2009, 48, 12272-12282.

16. Peterson, Y.; Wang, X. S.; Casey, P.*; Tropsha, A.* Discovery of geranylgeranyltransferase-I inhibitors with novel scaffolds by the means of Quantitative Structure-Activity Relationship modeling, virtual screening, and experimental validation. J. Med. Chem. 2009, 52, 4210-4220. (Co-ranked as first author)

17. Dong, Y. Z.; Shi, Q.*; Liu, Y-N.; Wang, X.; Bastow, K. F.*; Lee, K-H.* Antitumor agents. 266. Design, synthesis and biological evaluation of novel 2-(furan-2-yl)naphthalen-1-ol derivatives as potent and selective antibreast cancer agents. J. Med. Chem. 2009, 52, 3586-3590.

18. Tang, H.; Wang, X. S.; Huang, X-P.; Roth, B. L.; Butler, K. V.; Kozikowski, A. P.; Jung, M.; Tropsha, A.* Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening and experimental validation. J. Chem. Inf. Model. 2009, 49, 461-476.

19. Han, D.; Wang, S. X.; Weinstein, H.* Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs. Biochemistry 2008, 47, 7317-7321. (Elected as Hot Article)

20. Wang, X. S.; Tang, H.; Golbraikh, A.; Tropsha, A.* Combinatorial QSAR modeling of specificity and subtype selectivity of ligands binding to serotonin receptors 5HT1E and 5HT1F. J. Chem. Inf. Model. 2008, 48, 997-1013.

21. Hsieh, J-H.; Wang, X. S.; Teotico, D.; Golbraikh, A.; Tropsha, A.* Differentiation of AmpC beta-Lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening. J. Comput. Aided Mol. Des. 2008, 22, 593-609.

22. Filizola, M.*; Wang, S. X.; Weinstein, H.* Dynamic models of G-Protein Coupled Receptors dimers: Indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. J. Comput. Aided Mol. Des. 2006, 20, 405-416.

23. Wang, X. S.; Richards, N. G. J.* Computer-based strategy for modeling the interaction of AGRP and related peptide ligands with the AGRP-binding site of murine melanocortin receptors. (Review). Curr. Pharm. Des. 2005, 11, 345-356.

24. Joseph, C. G.; Wang, X. S.; Scott, J. W.; Bauzo, R. M.; Xiang, Z. M.; Richards, N. G. J.; Haskell-Luevano, C.* Stereochemical studies of the monocyclic agouti-related protein (103-122) Arg-Phe-Phe residues: conversion of a melanocortin-4 receptor antagonist into an agonist and results in the discovery of a potent and selective melanocortin-1 agonist. J. Med. Chem. 2004, 47, 6702-6710.

25. Wilczynski, A.; Wang, X. S.; Bauzo, R. M.; Xiang, Z. M.; Shaw, A. M.; Millard, W. J.; Richards, N. G. J.; Edison, A. S.; Haskell-Luevano, C.* Structural characterization and pharmacology of a potent (Cys101-Cys119, Cys110-Cys117) bicyclic agouti-related protein (AGRP) melanocortin receptor antagonist. J. Med. Chem. 2004, 47, 5662-5673. (Co-ranked as first author)

26. Wilczynski, A.; Wang, X. S.; Joseph, C. G.; Xiang, Z. M.; Bauzo, R. M.; Scott, J. W.; Sorensen, N. B.; Shaw, A. M.; Millard, W. J.; Richards, N. G. J.; Haskell-Luevano, C.* Identification of putative agouti-related protein(87-132)-melanocortin-4 receptor interactions by homology molecular modeling and validation using chimeric peptide ligands. J. Med. Chem. 2004, 47, 2194-2207. (Co-ranked as first author)

Selected Publications

Laboratory of Cheminfomatics and Drug Design

Refereed Articles

1. Fortunak, J. M. D.*; Emeje, M. O.; Kammendic, H.; Tilahun, E. L.; Wang, X. S. The business case for green chemistry in drug discovery. In: Green Chemistry Strategies for Drug Discovery Royal Society of Chemistry, 2015, Cambridge, In press.

2. Golbraikh, A.; Wang, X. S.; Zhu, H.; Tropsha, A.* Predictive QSAR modeling: Methods and applications in drug discovery and chemical risk assessment. In: Handbook of Computational Chemistry Springer-Verlag, 2011, Berlin Heidelberg, pp 1-36.

3. Tropsha, A.*; Wang, S. X. QSAR modeling of GPCR ligands: Methodologies and examples of applications. In: GPCRs: From Deorphanization to Lead Structure Identification Springer-Verlag, 2007, Leipzig, pp 49-73.

Book Chapters