Primary research articles

2023

• Carretero Chavez W, Krantz M, Klipp E, Kufareva I. kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models. BMC Bioinformatics 2023, 24:246, https://doi.org/10.1186/s12859-023-05329-6.

• Wedegaertner H, Bosompra O, Kufareva I, Trejo J. Divergent regulation of α-arrestin ARRDC3 function by ubiquitination. Mol Biol Cell. 2023 May 24:mbcE23020055. doi: 10.1091/mbc.E23-02-0055.

• Shroka TM, Kufareva I, Salanga CL, Handel TM. The dual-function chemokine receptor CCR2 drives migration and chemokine scavenging through distinct mechanisms. Sci Signal. 2023 Jan 31;16(770):eabo4314. doi: 10.1126/scisignal.abo4314. 

2021

• Navia-Pelaez JM, Choi SH, Dos Santos Aggum Capettini L, Xia Y, Gonen A, Agatisa-Boyle C, Delay L, Gonçalves Dos Santos G, Catroli GF, Kim J, Lu JW, Saylor B, Winkels H, Durant CP, Ghosheh Y, Beaton G, Ley K, Kufareva I, Corr M, Yaksh TL, Miller YI. Normalization of cholesterol metabolism in spinal microglia alleviates neuropathic pain. J Exp Med. 2021 Jul 5;218(7):e20202059. doi: 10.1084/jem.20202059.

• Ear J, Abd El-Hafeez AA, Roy S, Ngo T, Rajapakse N, Choi J, Khandelwal S, Ghassemian M, McCaffrey L, Kufareva I, Sahoo D, Ghosh P. A long isoform of GIV/Girdin contains a PDZ binding module that regulates localization and G-protein binding. J Biol Chem. 2021 Mar 3:100493. doi: 10.1016/j.jbc.2021.100493. 

• Ngo T, Wilkins BP, So SS, Keov P, Chahal KK, Finch AM, Coleman JLJ, Kufareva I*, Smith NJ*. Orphan receptor GPR37L1 remains unliganded. Nat Chem Biol. 2021 Mar 1. doi: 10.1038/s41589-021-00748-z - *co-corresponding authors

• Ngo T, Ilatovskiy AV, Stewart AG, Coleman JLJ, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. Retraction Note: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2021 Mar 1. doi: 10.1038/s41589-021-00746-1.

• Ortiz Zacarías NV, Chahal KK, Šimková T, van der Horst C, Zheng Y, Inoue A, Theunissen E, Mallee L, van der Es D, Louvel J, IJzerman AP, Handel TM*, Kufareva I*, Heitman LH*. Design and Characterization of an Intracellular Covalent Ligand for CC Chemokine Receptor 2. J Med Chem. 2021 Mar 11;64(5):2608-2621. doi: 10.1021/acs.jmedchem.0c01137 - *co-corresponding authors

2020

• Kalogriopoulos NA, Lopez-Sanchez I, Lin C, Ngo T, Midde KK, Roy S, Aznar N, Murray F, Garcia-Marcos M, Kufareva I, Ghassemian M, Ghosh P. Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi. Proc Natl Acad Sci U S A. 2020 Nov 17;117(46):28763-28774. doi: 10.1073/pnas.2004699117. 

• Swanson L, Katkar GD, Tam J, Pranadinata RF, Chareddy Y, Coates J, Anandachar MS, Castillo V, Olson J, Nizet V, Kufareva I, Das S, Ghosh P., TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin. Proc Natl Acad Sci U S A. 2020 Oct 27;117(43):26895-26906. doi: 10.1073/pnas.2011667117. 

• Stephens BS, Ngo T, Kufareva I*, Handel TM*. Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis. Science Signaling 2020, 13(640), eaay5024, DOI: 10.1126/scisignal.aay5024 - * co-corresponding authors

• Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM*, Kufareva I*. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol. 2020; 18(4):e3000656 - *co-corresponding authors

• Jaracz-Ros A, Bernadat G, Cutolo P, Gallego C, Gustavsson M, Cecon E, Baleux F, Kufareva I, Handel TM, Bachelerie F, Levoye A., Differential activity and selectivity of N-terminal modified CXCL12 chemokines at the CXCR4 and ACKR3 receptors. J Leukoc Biol. 2020;107(6):1123-1135. doi: 10.1002/JLB.2MA0320-383RR.

• Ear J, Saklecha A, Rajapakse N, Choi J, Ghassemian M, Kufareva I, Ghosh P. Tyrosine-Based Signals Regulate the Assembly of Daple⋅PARD3 Complex at Cell-Cell Junctions. iScience. 2020; 23(2):100859. 

• Nicola G, Kufareva I, Ilatovskiy AV, Abagyan R. Druggable exosites of the human kino-pocketome. J Comput Aided Mol Des. 2020; 34(3):219-230.

• Josephs TM, Keller AN, Khajehali E, DeBono A, Langmead CJ, Conigrave AD, Capuano B, Kufareva I, Gregory KJ, Leach K. Negative allosteric modulators of the human calcium-sensing receptor bind to overlapping and distinct sites within the 7-transmembrane domain. Br J Pharmacol. 2020; 177(8):1917-1930.

2019

• Kufareva I, Bestgen B, Brear P, Prudent R, Laudet B, Moucadel V, Ettaoussi M, Sautel CF, Krimm I, Engel M, Filhol O, Borgne ML, Lomberget T, Cochet C, Abagyan R. Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Sci Rep. 2019; 9(1):15893.

• Zhao BN, Campbell JJ, Salanga CL, Ertl LS, Wang Y, Yau S, Dang T, Zeng Y, McMahon JP, Krasinski A, Zhang P, Kufareva I, Handel TM, Charo IF, Singh R, Schall TJ. CCR2-Mediated Uptake of Constitutively Produced CCL2: A Mechanism for Regulating Chemokine Levels in the Blood. J Immunol. 2019, 203(12):pp3157-3165.

• Chahal, K.K., Li, J., Kufareva, I., Parle, M., Durden, D.L., Wechsler-Reya, R.J., Chen, C.C., Abagyan, R. Nilotinib, an approved leukemia drug, inhibits Smoothened signaling in Hedgehog-dependent medulloblastoma, PLoS ONE 2019, 14(9): e0214901 .

• Kalogriopoulos, N.A., S.D. Rees, T. Ngo, N.J. Kopcho, A.V. Ilatovskiy, N. Sun, E.A. Komives, G. Chang, P. Ghosh, I. Kufareva. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. PNAS 2019: p. 201906658.

• Regan D.P., Coy J.W., Chahal K.K., Chow L., Kurihara J.N., Guth A.M., Kufareva I., Dow S.W. The Angiotensin Receptor Blocker Losartan Suppresses Growth of Pulmonary Metastases via AT1R-Independent Inhibition of CCR2 Signaling and Monocyte Recruitment. J Immunol. 2019; 202(10):3087-3102. 

• Bestgen B, Krimm I, Kufareva I, Kamal AAM, Seetoh WG, Abell C, Hartmann RW, Abagyan R, Cochet C, Le Borgne M, Engel M, Lomberget T. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem. 2019; 62(4):1803-1816.

• Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 2. Structure-Based Optimization and Investigation of Effects Specific to the Allosteric Mode of Action. J Med Chem. 2019; 62(4):1817-1836.

2018

• Grimsey NJ, Narala R, Rada CC, Mehta S, Stephens BS, Kufareva I, Lapek J, Gonzalez DJ, Handel TM, Zhang J, Trejo J. A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep. 2018; 24(12):3312-3323.

• Keller, A.N., Kufareva, I., Josephs, T.M., Diao, J., Mai, V.T., Conigrave, A.D., Christopoulos, A., Gregory, K.J., Leach, K. Identification of Global and Ligand-Specific Calcium Sensing Receptor Activation Mechanisms. Mol Pharmacol. 2018, 93(6):619-630.

2017

• Aznar, N., Ear, J., Dunkel, Y., Sun, N., Satterfield, K., He, F., Kalogriopoulos, N.A., Lopez-Sanchez, I., Ghassemian, M., Sahoo, D., Kufareva, I., Ghosh, P. Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple. Sci Signal. 2018, 11(519), pii: eaao4220.

• Zheng, Y., G. W. Han, R. Abagyan, B. Wu, R.C. Stevens, V. Cherezov, I. Kufareva*, and T.M. Handel*, Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity, 2017, 46(6), 1005-17.e5 - * co-corresponding author

• Gustavsson, M., L. Wang, N. van Gils, B.S. Stephens, P. Zhang, T. Schall, S. Yang, R. Abagyan, M.R. Chance, I. Kufareva*, and T.M. Handel*, Structural basis of ligand interaction with atypical chemokine receptor 3. Nature Communications, 2017, 8, 14135 - * co-corresponding author

• Ngo, T., A.V. Ilatovskiy, A.G. Stewart, J.L.J. Coleman, F.M. McRobb, R.P. Riek, R.M. Graham, R. Abagyan, I. Kufareva*, and N.J. Smith*, Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nature Chemical Biology, 2017, 13(2), 235-242 - * co-corresponding author

2016

• Zheng, Y., L. Qin, N.V.O. Zacarías, H. de Vries, G.W. Han, M. Gustavsson, M. Dabros, C. Zhao, R.J. Cherney, P. Carter, D. Stamos, R. Abagyan, V. Cherezov, R.C. Stevens, A.P. Ijzerman, L.H. Heitman, A. Tebben, I. Kufareva*, and T.M. Handel*, Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature, 2016, 540:458-461 - * co-corresponding author

• Hua T, Vemuri K, Pu M, Qu L, Han GW, Wu Y, Zhao S, Shui W, Li S, Korde A, Laprairie RB, Stahl EL, Ho JH, Zvonok N, Zhou H, Kufareva I, Wu B, Zhao Q, Hanson MA, Bohn LM, Makriyannis A, Stevens RC, Liu ZJ. Crystal Structure of the Human Cannabinoid Receptor CB1. Cell, 2016, 167(3), 750-762.

• Aznar N, Patel A, Rohena CC, Dunkel Y, Joosen LP, Taupin V, Kufareva I, Farquhar MG, Ghosh P. AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin. Elife, 2016, 5, pii: e20795.

• Wescott, M.P., Kufareva, I., Paes, C., Goodman, J.R., Thaker, Y., Puffer, B.A., Berdougo, E., Rucker, J.B., Handel, T,M,, Doranz, B.J. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A, 2016, 113(35), 9928-33.

• Leach, K.; Gregory, K. J.; Kufareva, I.; Khajehali, E.; Cook, A. E.; Abagyan, R.; Conigrave, A. D.; Sexton, P. M.; Christopoulos, A., Towards a structural understanding of allosteric drugs at the human calcium sensing receptor. Cell Research 2016, 26:574-92.

2015

• Lenoir, M.; Kufareva, I.; Abagyan, R.; Overduin, M., Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes 2015, 5 (4), 646.

• O'Hayre, M.; Inoue, A.; Kufareva, I.; Wang, Z.; Mikelis, C. M.; Drummond, R. A.; Avino, S.; Finkel, K.; Kalim, K. W.; DiPasquale, G.; Guo, F.; Aoki, J.; Zheng, Y.; Lionakis, M. S.; Molinolo, A. A.; Gutkind, J. S., Inactivating mutations in GNA13 and RHOA in Burkitt's lymphoma and diffuse large B-cell lymphoma: a tumor suppressor function for the G[alpha] 13/RhoA axis in B cells. Oncogene 2015.

• Qin, L.; Kufareva, I.* ; Holden, L. G.; Wang, C.; Zheng, Y.; Zhao, C.; Fenalti, G.; Wu, H.; Han, G. W.; Cherezov, V., Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science 2015, 347 (6226), 1117-1122 - * co-principal and co-corresponding author

• Lo, I.-C.; Gupta, V.; Midde, K. K.; Taupin, V.; Lopez-Sanchez, I.; Kufareva, I.; Abagyan, R.; Randazzo, P. A.; Farquhar, M. G.; Ghosh, P., Activation of Gαi at the Golgi by GIV/Girdin Imposes Finiteness in Arf1 Signaling. Developmental cell 2015, 33 (2), 189-203.

• Husby, J.; Bottegoni, G.; Kufareva, I.; Abagyan, P. D. R.; Cavalli, A., Structure-based predictions of activity cliffs. Journal of chemical information and modeling 2015, 55(5), 1062-76.

• Hanes, M. S.; Salanga, C. L.; Chowdry, A. B.; Comerford, I.; McColl, S. R.; Kufareva, I.; Handel, T. M., Dual Targeting of the Chemokine Receptors CXCR4 and ACKR3 with Novel Engineered Chemokines. Journal of Biological Chemistry 2015, jbc. M115. 675108.

2014

• McRobb, F. M.; Sahagún, V.; Kufareva, I.; Abagyan, R., In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environmental science & technology 2014, 48 (3), 1964-72.

• McRobb, F. M.; Kufareva, I.*; Abagyan, R.*, In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. Toxicological Sciences 2014, kfu114 - * co-corresponding author

• Lin, C.; Ear, J.; Midde, K.; Lopez-Sanchez, I.; Aznar, N.; Garcia-Marcos, M.; Kufareva, I.; Abagyan, R.; Ghosh, P., Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Molecular biology of the cell 2014, 25 (22), 3654-3671.

• Kufareva, I.* ; Stephens, B S.; Holden, L.G.; Qin, L.; Zhao, C.; Kawamura, T.; Abagyan, R.; Handel, T.M., Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: Molecular modeling and experimental validation. Proceedings of the National Academy of Sciences 2014, 111 (50), E5363-E5372 -- * principal and co-corresponding author.

• Kufareva, I.; Lenoir, M.; Dancea, F.; Sridhar, P.; Raush, E.; Bissig, C.; Gruenberg, J.; Abagyan, R.; Overduin, M., Discovery of novel membrane binding structures and functions. Biochemistry and Cell Biology 2014, 92 (6), 555-563.

• Kufareva, I.; Katritch, V.; Stevens, R. C.; Abagyan, R., Advances in GPCR modeling evaluated by the GPCR dock 2013 assessment: meeting new challenges. Structure 2014, 22 (8), 1120-1139.

• Kawamura, T.; Stephens, B.; Qin, L.; Yin, X.; Dores, M. R.; Smith, T. H.; Grimsey, N.; Abagyan, R.; Trejo, J.; Kufareva, I., Fuster, M.M., Salanga, C.L., Handel, T.M. A general method for site specific fluorescent labeling of recombinant chemokines. PloS one 2014, 9 (1).

• Gabrielsen, M.; Kurczab, R.; Siwek, A.; Wolak, M.; Ravna, A. W.; Kristiansen, K.; Kufareva, I.; Abagyan, R.; Nowak, G.; Chilmonczyk, Z., Identification of novel serotonin transporter compounds by virtual screening. Journal of chemical information and modeling 2014, 54 (3), 933-943.

• Acharya, C.; Kufareva, I.; Ilatovskiy, A. V.; Abagyan, R., PeptiSite: a structural database of peptide binding sites in 4D. Biochemical and biophysical research communications 2014, 445 (4), 717-723. 

2013

• Ziarek, J. J.; Getschman, A. E.; Butler, S. J.; Taleski, D.; Stephens, B.; Kufareva, I.; Handel, T. M.; Payne, R. J.; Volkman, B. F., Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery. ACS chemical biology 2013, 8 (9), 1955-1963.

• Tan, Q.; Zhu, Y.; Li, J.; Chen, Z.; Han, G. W.; Kufareva, I.; Li, T.; Ma, L.; Fenalti, G.; Li, J., Structure of the CCR5 chemokine receptor - HIV entry inhibitor Maraviroc complex. Science 2013, 341 (6152), 1387-1390.

• Shah, M. B.; Kufareva, I.; Pascual, J.; Zhang, Q.; Stout, C. D.; Halpert, J. R., A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states. Journal of Pharmacology and Experimental Therapeutics 2013, 346 (1), 113-120.

• Lindin, I.; Wuxiuer, Y.; Kufareva, I.; Abagyan, R.; Moens, U.; Sylte, I.; Ravna, A. W., Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor. Biol. Med. Model 2013, 10, 56.

• Katiyar, S.; Kufareva, I.; Behera, R.; Thomas, S. M.; Ogata, Y.; Pollastri, M.; Abagyan, R.; Mensa-Wilmot, K., Lapatinib- binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PloS one 2013, 8 (2), e56150.

• Gabrielsen, M.; Wołosewicz, K.; Zawadzka, A.; Kossakowski, J.; Nowak, G.; Wolak, M.; Stachowicz, K.; Siwek, A.; Ravna, A. W.; Kufareva, I., Kozerski, L., Bednarek, E., Sitkowski, J., Bocian, W., Abagyan, R., Bojarski, A.J., Sylte, I., Chilmonczyk, Z. Synthesis, Antidepressant Evaluation and Docking Studies of Long‐Chain Alkylnitroquipazines as Serotonin Transporter Inhibitors. Chemical biology & drug design 2013, 81 (6), 695-706.

• Davydov, D. R.; Davydova, N. Y.; Sineva, E. V.; Kufareva, I.; Halpert, J. R., Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of alpha-naphthoflavone. Biochemical Journal 2013, 453 (2), 219-230.

• Bissig, C.; Lenoir, M.; Velluz, M.-C.; Kufareva, I.; Abagyan, R.; Overduin, M.; Gruenberg, J., Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Developmental cell 2013, 25 (4), 364-373. 

2012

• Sager, G.; Ørvoll, E. Ø.; Lysaa, R. A.; Kufareva, I.; Abagyan, R.; Ravna, A. W., Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. Journal of medicinal chemistry 2012, 55 (7), 3049-3057.

• Kufareva, I. * ; Ilatovskiy, A. V.; Abagyan, R., Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic acids research 2012, 40 (D1), D535-D540 - *principal and co-corresponding author

• Kufareva, I.; Chen, Y.-C.; Ilatovskiy, A. V.; Abagyan, R., Compound activity prediction using models of binding pockets or ligand properties in 3D. Current topics in medicinal chemistry 2012, 12 (17), 1869-1882.

• Jarończyk, M.; Wołosewicz, K.; Gabrielsen, M.; Nowak, G.; Kufareva, I.; Mazurek, A. P.; Ravna, A. W.; Abagyan, R.; Bojarski, A. J.; Sylte, I., Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. European Journal of Medicinal Chemistry 2012, 49, 200-210.

• Gabrielsen, M.; Kurczab, R.; Ravna, A. W.; Kufareva, I.; Abagyan, R.; Chilmonczyk, Z.; Bojarski, A. J.; Sylte, I., Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. European journal of medicinal chemistry 2012, 47, 24-37. 

2011

• Lin, C.; Ear, J.; Pavlova, Y.; Mittal, Y.; Kufareva, I.; Ghassemian, M.; Abagyan, R.; Garcia-Marcos, M.; Ghosh, P., Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Science Signaling 2011, 4 (192), ra64-ra64.

• Kufareva, I.; Rueda, M.; Katritch, V.; Dock, G.; Stevens, R. C.; Abagyan, R., Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 2011, 19 (8), 1108-1126.

• Katritch, V.; Kufareva, I.; Abagyan, R., Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology 2011, 60 (1), 108-115. 

2010

• 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. 

2008

• Lee, H. S.; Choi, J.; Kufareva, I.; Abagyan, R.; Filikov, A.; Yang, Y.; Yoon, S., Optimization of high throughput virtual screening by combining shape-matching and docking methods. Journal of chemical information and modeling 2008, 48 (3), 489-497.

• Kufareva, I.; Abagyan, R., Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. Journal of medicinal chemistry 2008, 51 (24), 7921-7932.

• Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R., A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). Journal of computer-aided molecular design 2008, 22 (5), 311-325.

• Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R., Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. Journal of medicinal chemistry 2008, 52 (2), 397-406.

1998-2007

• Outeiro, T. F.; Kontopoulos, E.; Altmann, S. M.; Kufareva, I.; Strathearn, K. E.; Amore, A. M.; Volk, C. B.; Maxwell, M. M.; Rochet, J.-C.; McLean, P. J., Young, A. B., Abagyan, R., Feany, M. B., Hyman, B. T., Kazantsev, A. G. Sirtuin 2 inhibitors rescue α-synuclein-mediated toxicity in models of Parkinson's disease. Science 2007, 317 (5837), 516-519.

• Kufareva, I.; Budagyan, L.; Raush, E.; Totrov, M.; Abagyan, R., PIER: protein interface recognition for structural proteomics. Proteins: Structure, Function, and Bioinformatics 2007, 67 (2), 400-417.

• Hayashi, T.; Mo, J.-H.; Gong, X.; Rossetto, C.; Jang, A.; Beck, L.; Elliott, G. I.; Kufareva, I.; Abagyan, R.; Broide, D. H., 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proceedings of the National Academy of Sciences 2007, 104 (47), 18619-18624.

• Kufareva, I.; Yevtushenko, N.; Petrenko, A. Design of Tests for Nondeterministic Machines with Respect to Reduction. Automatic Control and Computer Sciences, Allerton Press Inc. 1998, 3.

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 and....now, 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.