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Small-Molecule Protein Interactions

The aims of these projects are to 1) efficiently deploy computational chemistry tools on DoD high-performance computing assets, 2) model how enzymes process substrate molecules, and 3) develop simulation techniques to accurately calculate changes in drug- or protein-binding free energies. We use these methods to study human serum paraoxonase 1 as a potential bioscavenger for nerve agents, binding of small molecules to Botulinum neurotoxins, and mutations that confer resistance in influenza viruses.



AbdulHameed, M. D., R. Liu, P. Schyman, D. Sachs, Z. Xu, V. Desai, and A. Wallqvist. ToxProfiler: toxicity-target profiler based on chemical similarity. Computational Toxicology. 2021 May; 18:100162. [PDF, Link]

Khavrutskii, I. V., and A. Wallqvist. Beta-aminoalcohols as potential reactivators of aged sarin-/soman-inhibited acetylcholinesterase. ChemistrySelect. 2017 February 13; 2(5):1885-1890. [PDF, DTIC]

Khavrutskii, I. V., P. M. Legler, A. M. Friedlander, and A. Wallqvist. A reaction path study of the catalysis and inhibition of the Bacillus anthracis CapD gamma-glutamyl transpeptidase. Biochemistry. 2014 November 11; 53(44):6954-6967. [PDF, PubMed]

Liu, J., G. J. Tawa, and A. Wallqvist. Identifying cytochrome P450 functional networks and their allosteric regulatory elements. PLOS ONE. 2013 December 3; 8(12):e81980. [PDF, PubMed]

Khavrutskii, I. V., J. B. Smith, and A. Wallqvist. Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization. Journal of Chemical Physics. 2013 October 25; 139(16):165104. [PDF, PubMed]

Hu, X., J. R. Compton, M. D. AbdulHameed, C. L. Marchand, K. L. Robertson, D. H. Leary, A. Jadhav, J. R. Hershfield, A. Wallqvist, A. M. Friedlander, and P. M. Legler. 3-substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening. Journal of Medicinal Chemistry. 2013 July 1; 56(13):5275-5287. [PDF, PubMed]

Chaudhury, S., M. D. AbdulHameed, N. Singh, G. Tawa, P. M. D'haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozack, J. L. Dankmeyer, K. Amemiya, S. Daefler, and A. Wallqvist. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLOS ONE. 2013 May 21; 8(5):e63369. [PDF, PubMed]

Ripoll, D. R., I. V. Khavrutskii, S. Chaudhury, J. Liu, R. A. Kuschner, A. Wallqvist, and J. Reifman. Quantitative predictions of binding free energy changes in drug-resistant influenza neuraminidase. PLOS Computational Biology. 2012 August 30; 8(8):e1002665. [PDF, PubMed]

Cardellina, J. H., V. Roxas-Duncan, V. Montgomery, V. Eccard, Y. Campbell, X. Hu, I. Khavrutskii, G. Tawa, A. Wallqvist, J. Gloer, N. Phatak, U. Hoeller, A. Soman, B. Joshi, S. Hein, D. Wicklow, and L. A. Smith. Fungal bis-naphthopyrones as inhibitors of botulinum neurotoxin serotype A. ACS Medicinal Chemistry Letters. 2012 April 2; 3(5):387-391. [PDF, PubMed]

Sun, H., G. Tawa, and A. Wallqvist. Classification of scaffold-hopping approaches. Drug Discovery Today. 2012 April; 17(7-8):310-324. [PDF, PubMed]

AbdulHameed, M. D., S. Chaudhury, N. Singh, H. Sun, A. Wallqvist, and G. J. Tawa. Exploring polypharmacology using a ROCS-based target fishing approach. Journal of Chemical Information and Modeling. 2012 February 27; 52(2):492-505. [PDF, PubMed]

Singh, N., H. Sun, S. Chaudhury, M. D. AbdulHameed, A. Wallqvist, and G. Tawa. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. Journal of Cheminformatics. 2012 February 8; 4:4. [PDF, PubMed]

Hu, X., P. M. Legler, I. Khavrutskii, A. Scorpio, J. R. Compton, K. L. Robertson, A. M. Friedlander, and A. Wallqvist. Probing the donor and acceptor substrate specificity of the y-glutamyl transpeptidase. Biochemistry. 2012 January 17; 51(6):1199-1212. [PDF, PubMed]

Khavrutskii, I., and A. Wallqvist. Improved binding free energy predictions from single-reference thermodynamic integration augmented with Hamiltonian replica exchange. Journal of Chemical Theory and Computation. 2011 August 15; 7(9):3001-3011. [PDF, PubMed]

Cardellina, J. H., R. Vieira, V. Eccard, J. Skerry, V. Montgomery, Y. Campbell, V. Roxas-Duncan, W. Leister, C. A. LeClair, D. J. Maloney, D. Padula, G. Pescitelli, I. Khavrutskii, X. Hu, A. Wallqvist, and L. A. Smith. Separation of Betti reaction product enantiomers: absolute configuration and inhibition of botulinum neurotoxin A. ACS Medicinal Chemistry Letters. 2011 March; 2(5):396-401. [PDF, PubMed]

Khavrutskii, I., and A. Wallqvist. Computing relative free energies of solvation using single reference thermodynamic integration augmented with Hamiltonian replica exchange. Journal of Chemical Theory and Computation. 2010 October 21; 6(11):3427-3441. [PDF, PubMed]

Hu, X., X. Jiang, D. E. Lenz, D. M. Cerasoli, and A. Wallqvist. In silico analyses of substrate interactions with human serum paraoxonase 1. Proteins. 2009 May 1; 75(2):486-498. [PDF, PubMed]

Jiang, X., K. Kumar, X. Hu, A. Wallqvist, and J. Reifman. DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chemistry Central Journal. 2008 September 8; 2(1):18. [PDF, PubMed]

Zhang, S., K. Kumar, X. Jiang, A. Wallqvist, and J. Reifman. DOVIS: an implementation for high-throughput virtual screening using AutoDock. BMC Bioinformatics. 2008 February 29; 9:126. [PDF, PubMed]

Jiang, X., K. Kumar, A. Wallqvist, and J. Reifman. DOVIS: a tool for high-throughput virtual screening. Proceedings of the HPCMP Users Group Conference. Pittsburgh, PA. 2007 June 18-22; 421-424. [PDF, DTIC]