Primary research articles












  • Park, S.-J.; Kufareva, I.; Abagyan, R., Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. Journal of computer-aided molecular design 2010, 24 (5), 459-471.
  • Katritch, V.; Jaakola, V.-P.; Lane, J. R.; Lin, J.; IJzerman, A. P.; Yeager, M.; Kufareva, I.; Stevens, R. C.; Abagyan, R., Structure-based discovery of novel chemotypes for adenosine A2A receptor antagonists. Journal of medicinal chemistry 2010, 53 (4), 1799-1809.
  • Grigoryan, A.; Kufareva, I.; Totrov, M.; Abagyan, R., Spatial chemical distance based on atomic property fields. Journal of computer-aided molecular design 2010, 24 (3), 173-182.



Review and invited articles

  • Kufareva, I. * , Gustavsson, M., Zheng, Y., Stephens, B.S., Handel, T.M. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annual Review of Biophysics, 2017, 46, 175-198 - * principal and co-corresponding author
  • Ghosh, P., P. Rangamani, and I. Kufareva, The GAPs, GEFs, GDIs, GEMs: new kids on the G protein signaling block. Cell Cycle, 2017;16(7): 607-612
  • Kufareva, I. * Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol. 2016 Oct;30:27-37. doi: 10.1016/j.coph.2016.07.006 - * principal and corresponding author
  • Ngo, T.; Kufareva, I.; Coleman, J. L. J.; Graham, R. M.; Abagyan, R.; Smith, N. J., Identifying ligands at orphan GPCRs: current status using structure-based approaches. British Journal of Pharmacology, 2016.
  • Kufareva, I.; Salanga, C. L.; Handel, T. M., Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies. Immunology and Cell Biology 2015, 93 (4), 372-383. O'Hayre, M.; Vázquez-Prado, J.; Kufareva, I.; Stawiski, E. W.; Handel, T. M.; Seshagiri, S.; Gutkind, J. S., The emerging mutational landscape of G proteins and G-protein-coupled receptors in cancer. Nature Reviews Cancer 2013, 13 (6), 412-424.
  • Montaner, S.; Kufareva, I.; Abagyan, R.; Gutkind, J. S., Molecular Mechanisms Deployed by Virally Encoded G Protein Coupled Receptors in Human Diseases. Annual Review of Pharmacology and Toxicology 2013, 53, 331-354. Ilatovskiy, A. V.; Abagyan, R.; Kufareva, I. * , Quantum mechanics approaches to drug research in the era of structural chemogenomics. International Journal of Quantum Chemistry 2013, 113 (12), 1669-1675 - * corresponding author

Book chapters

  • Kufareva, I., Gustavsson, M., Holden, L.G., Qin, L., Zheng, Y., Handel, T.M. Disulfide Trapping for Modeling and Structure Determination of Receptor:Chemokine Complexes, in Methods in Enzymology, T.M. Handel, Ed. (Academic Press, 2016), Vol. 570, pp. 389-420.
  • Kufareva, I.; Handel, T. M.; Abagyan, R., Experiment-Guided Molecular Modeling of Protein–Protein Complexes Involving GPCRs. In G Protein-Coupled Receptors in Drug Discovery, Filizola, M., Ed. Springer New York: 2015; Vol. 1335, pp 295-311.
  • Kufareva, I. * ; Abagyan, R.; Handel, T. M., Role of 3D Structures in Understanding, Predicting, and Designing Molecular Interactions in the Chemokine Receptor Family. In Chemokines, Tschammer, N., Ed. Springer International Publishing: 2015; Vol. 14, pp 41-85 - * principal and corresponding author
  • Kufareva, I. * ; Stephens, B.; Gilliland, C. T.; Wu, B.; Fenalti, G.; Hamel, D. J.; Stevens, R. C.; Abagyan, R.; Handel, T. M., A Novel Approach to Quantify G-Protein-Coupled Receptor Dimerization Equilibrium Using Bioluminescence Resonance Energy Transfer. In Chemokines: Methods and Protocols, Cardona, A. E.; Ubogu, E. E., Eds. Springer Science+Business Media: New York, 2013; Vol. 1013, pp 93-127 - * principal and co-corresponding author
  • Kufareva, I.; Abagyan, R., Methods of Protein Structure Comparison. In Homology Modeling, Orry, A. J. W.; Abagyan, R., Eds. Humana Press: 2012; Vol. 857, pp 231-257.
  • Abagyan, R.; Chen, W.; Kufareva, I., Docking, Screening and Selectivity Prediction for Small-molecule Nuclear Receptor Modulators. In Computational Approaches to Nuclear Receptors, Cozzini, P.; Kellogg, G. E., Eds. RSC Drug Discovery: 2012; pp 84-109.
  • Kufareva, I.; Abagyan, R., Predicting Molecular Interactions in Structural Proteomics. In Computational Protein-Protein Interactions, Nussinov, R.; Schreiber, G., Eds. CRC Press: 2009; pp 185-209.
  • Abagyan, R.; Kufareva, I., The Flexible Pocketome Engine for Structural Chemogenomics. In Chemogenomics, Jacoby, E., Ed. Humana Press: 2009; Vol. 575, pp 249-279.
  • Stoffel, D.; Karibaev, E.; Kufareva, I.; Kunz, W., Equivalence Checking of Arithmetic Circuits. In Advanced Formal Verification, Drechsler, R., Ed. Kluwer Academic Publishers: Gremen, Germany, 2004; pp 77-123.