Irina Kufareva

Title(s)Associate Adjunct Professor, School of Pharmacy and Pharmaceutical Science
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    It's a tug of war: structure, consequences, and inhibition of CXCR4 and ACKR3 responses to lymphocyte chemoattractant CXCL12
    NIH R01AI161880Apr 15, 2021 - Mar 31, 2026
    Role: Co-Principal Investigator
    Spatiotemporally resolved architecture of G protein signaling downstream of CXCR4, the driver of lymphocyte migration
    NIH R21AI156662Apr 1, 2021 - Mar 31, 2023
    Role: Principal Investigator
    Computationally informed discovery of scavenging-sparing inhibitors of CC chemokine receptor 2
    NIH R21AI149369Jun 4, 2020 - May 31, 2022
    Role: Principal Investigator
    Signaling circuits that drive cell movement and ligand scavenging by chemokine receptor CCR2
    NIH R01GM136202May 1, 2020 - Jan 31, 2024
    Role: Co-Principal Investigator
    Chemokine interaction with CXCR4 and ACKR3: structure and activation mechanisms
    NIH R01GM117424Sep 15, 2016 - May 31, 2020
    Role: Principal Investigator
    The structural plasticity of chemokine and gp120 recognition by CCR5
    NIH R01AI118985May 11, 2015 - Apr 30, 2021
    Role: Principal Investigator

    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. bioRxiv. 2024 Feb 12. Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. PMID: 38014122; PMCID: PMC10680698.
      View in: PubMed   Mentions:
    2. Ligand-Dependent Mechanisms of C-C Chemokine Receptor 5 (CCR5) Trafficking Revealed by APEX2 Proximity Labeling Proteomics. bioRxiv. 2023 Nov 03. Gu S, Maurya S, Lona A, Borrega-Roman L, Salanga C, Gonzalez DJ, Kufareva I, Handel TM. PMID: 37961097; PMCID: PMC10635066.
      View in: PubMed   Mentions:
    3. kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models. BMC Bioinformatics. 2023 Jun 12; 24(1):246. Carretero Chavez W, Krantz M, Klipp E, Kufareva I. PMID: 37308855; PMCID: PMC10258968.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    4. Divergent regulation of α-arrestin ARRDC3 function by ubiquitination. Mol Biol Cell. 2023 08 01; 34(9):ar93. Wedegaertner H, Bosompra O, Kufareva I, Trejo J. PMID: 37223976; PMCID: PMC10398895.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    5. The dual-function chemokine receptor CCR2 drives migration and chemokine scavenging through distinct mechanisms. Sci Signal. 2023 01 31; 16(770):eabo4314. Shroka TM, Kufareva I, Salanga CL, Handel TM. PMID: 36719944; PMCID: PMC10091583.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    6. Normalization of cholesterol metabolism in spinal microglia alleviates neuropathic pain. J Exp Med. 2021 07 05; 218(7). 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. PMID: 33970188; PMCID: PMC8111462.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    7. Retraction Note: Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2021 Apr; 17(4):501. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JLJ, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. PMID: 33649604; PMCID: PMC7990710.
      View in: PubMed   Mentions: 1     Fields:    
    8. A long isoform of GIV/Girdin contains a PDZ-binding module that regulates localization and G-protein binding. J Biol Chem. 2021 Jan-Jun; 296:100493. 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. PMID: 33675748; PMCID: PMC8042451.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    9. Orphan receptor GPR37L1 remains unliganded. Nat Chem Biol. 2021 04; 17(4):383-386. Ngo T, Wilkins BP, So SS, Keov P, Chahal KK, Finch AM, Coleman JLJ, Kufareva I, Smith NJ. PMID: 33649602; PMCID: PMC8015687.
      View in: PubMed   Mentions: 2     Fields:    
    10. Design and Characterization of an Intracellular Covalent Ligand for CC Chemokine Receptor 2. J Med Chem. 2021 03 11; 64(5):2608-2621. 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. PMID: 33600174; PMCID: PMC7958898.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    11. Receptor tyrosine kinases activate heterotrimeric G proteins via phosphorylation within the interdomain cleft of Gαi. Proc Natl Acad Sci U S A. 2020 11 17; 117(46):28763-28774. 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. PMID: 33139573; PMCID: PMC7682395.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    12. TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin. Proc Natl Acad Sci U S A. 2020 10 27; 117(43):26895-26906. 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. PMID: 33055214; PMCID: PMC7604444.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    13. Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis. Sci Signal. 2020 07 14; 13(640). Stephens BS, Ngo T, Kufareva I, Handel TM. PMID: 32665413; PMCID: PMC7437921.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsCells
    14. Differential activity and selectivity of N-terminal modified CXCL12 chemokines at the CXCR4 and ACKR3 receptors. J Leukoc Biol. 2020 06; 107(6):1123-1135. Jaracz-Ros A, Bernadat G, Cutolo P, Gallego C, Gustavsson M, Cecon E, Baleux F, Kufareva I, Handel TM, Bachelerie F, Levoye A. PMID: 32374043; PMCID: PMC7540625.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    15. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol. 2020 04; 18(4):e3000656. Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. PMID: 32271748; PMCID: PMC7173943.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    16. Negative allosteric modulators of the human calcium-sensing receptor bind to overlapping and distinct sites within the 7-transmembrane domain. Br J Pharmacol. 2020 04; 177(8):1917-1930. Josephs TM, Keller AN, Khajehali E, DeBono A, Langmead CJ, Conigrave AD, Capuano B, Kufareva I, Gregory KJ, Leach K. PMID: 31881094; PMCID: PMC7070164.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    17. Tyrosine-Based Signals Regulate the Assembly of Daple⋅PARD3 Complex at Cell-Cell Junctions. iScience. 2020 Feb 21; 23(2):100859. Ear J, Saklecha A, Rajapakse N, Choi J, Ghassemian M, Kufareva I, Ghosh P. PMID: 32058970; PMCID: PMC7005484.
      View in: PubMed   Mentions: 6  
    18. Druggable exosites of the human kino-pocketome. J Comput Aided Mol Des. 2020 03; 34(3):219-230. Nicola G, Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 31925639; PMCID: PMC7082431.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    19. Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors. Sci Rep. 2019 11 04; 9(1):15893. 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. PMID: 31685885; PMCID: PMC6828666.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    20. CCR2-Mediated Uptake of Constitutively Produced CCL2: A Mechanism for Regulating Chemokine Levels in the Blood. J Immunol. 2019 12 15; 203(12):3157-3165. 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. PMID: 31676674; PMCID: PMC7028331.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    21. Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma. PLoS One. 2019; 14(9):e0214901. Chahal KK, Li J, Kufareva I, Parle M, Durden DL, Wechsler-Reya RJ, Chen CC, Abagyan R. PMID: 31539380; PMCID: PMC6754133.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    22. Structural basis for GPCR-independent activation of heterotrimeric Gi proteins. Proc Natl Acad Sci U S A. 2019 08 13; 116(33):16394-16403. Kalogriopoulos NA, Rees SD, Ngo T, Kopcho NJ, Ilatovskiy AV, Sun N, Komives EA, Chang G, Ghosh P, Kufareva I. PMID: 31363053; PMCID: PMC6697900.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    23. The Angiotensin Receptor Blocker Losartan Suppresses Growth of Pulmonary Metastases via AT1R-Independent Inhibition of CCR2 Signaling and Monocyte Recruitment. J Immunol. 2019 05 15; 202(10):3087-3102. Regan DP, Coy JW, Chahal KK, Chow L, Kurihara JN, Guth AM, Kufareva I, Dow SW. PMID: 30971441; PMCID: PMC6504574.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    24. 2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site. J Med Chem. 2019 02 28; 62(4):1803-1816. 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. PMID: 30689953; PMCID: PMC7667462.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    25. 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 02 28; 62(4):1817-1836. Bestgen B, Kufareva I, Seetoh W, Abell C, Hartmann RW, Abagyan R, Le Borgne M, Filhol O, Cochet C, Lomberget T, Engel M. PMID: 30689946; PMCID: PMC7579840.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    26. A Tyrosine Switch on NEDD4-2 E3 Ligase Transmits GPCR Inflammatory Signaling. Cell Rep. 2018 09 18; 24(12):3312-3323.e5. Grimsey NJ, Narala R, Rada CC, Mehta S, Stephens BS, Kufareva I, Lapek J, Gonzalez DJ, Handel TM, Zhang J, Trejo J. PMID: 30232011; PMCID: PMC6226018.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    27. Dual Action Calcium-Sensing Receptor Modulator Unmasks Novel Mode-Switching Mechanism. ACS Pharmacol Transl Sci. 2018 Nov 09; 1(2):96-109. Gregory KJ, Kufareva I, Keller AN, Khajehali E, Mun HC, Goolam MA, Mason RS, Capuano B, Conigrave AD, Christopoulos A, Leach K. PMID: 32219206; PMCID: PMC7089027.
      View in: PubMed   Mentions: 7  
    28. Identification of Global and Ligand-Specific Calcium Sensing Receptor Activation Mechanisms. Mol Pharmacol. 2018 06; 93(6):619-630. Keller AN, Kufareva I, Josephs TM, Diao J, Mai VT, Conigrave AD, Christopoulos A, Gregory KJ, Leach K. PMID: 29636377; PMCID: PMC5941188.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    29. Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple. Sci Signal. 2018 02 27; 11(519). Aznar N, Ear J, Dunkel Y, Sun N, Satterfield K, He F, Kalogriopoulos NA, Lopez-Sanchez I, Ghassemian M, Sahoo D, Kufareva I, Ghosh P. PMID: 29487190; PMCID: PMC5862031.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    30. Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV. Immunity. 2017 06 20; 46(6):1005-1017.e5. Zheng Y, Han GW, Abagyan R, Wu B, Stevens RC, Cherezov V, Kufareva I, Handel TM. PMID: 28636951; PMCID: PMC5572563.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimalsCells
    31. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys. 2017 05 22; 46:175-198. Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. PMID: 28532213; PMCID: PMC5764094.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    32. The GAPs, GEFs, GDIs and…now, GEMs: New kids on the heterotrimeric G protein signaling block. Cell Cycle. 2017 Apr 03; 16(7):607-612. Ghosh P, Rangamani P, Kufareva I. PMID: 28287365; PMCID: PMC5397260.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    33. Structural basis of ligand interaction with atypical chemokine receptor 3. Nat Commun. 2017 01 18; 8:14135. Gustavsson M, Wang L, van Gils N, Stephens BS, Zhang P, Schall TJ, Yang S, Abagyan R, Chance MR, Kufareva I, Handel TM. PMID: 28098154; PMCID: PMC5253664.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    34. Orphan receptor ligand discovery by pickpocketing pharmacological neighbors. Nat Chem Biol. 2017 02; 13(2):235-242. Ngo T, Ilatovskiy AV, Stewart AG, Coleman JL, McRobb FM, Riek RP, Graham RM, Abagyan R, Kufareva I, Smith NJ. PMID: 27992882; PMCID: PMC5247308.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    35. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016 12 15; 540(7633):458-461. Zheng Y, Qin L, Zacarías NV, de Vries H, Han GW, Gustavsson M, Dabros M, Zhao C, Cherney RJ, Carter P, Stamos D, Abagyan R, Cherezov V, Stevens RC, IJzerman AP, Heitman LH, Tebben A, Kufareva I, Handel TM. PMID: 27926736; PMCID: PMC5159191.
      View in: PubMed   Mentions: 116     Fields:    Translation:HumansCells
    36. AMP-activated protein kinase fortifies epithelial tight junctions during energetic stress via its effector GIV/Girdin. Elife. 2016 11 04; 5. Aznar N, Patel A, Rohena CC, Dunkel Y, Joosen LP, Taupin V, Kufareva I, Farquhar MG, Ghosh P. PMID: 27813479; PMCID: PMC5119889.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    37. Crystal Structure of the Human Cannabinoid Receptor CB1. Cell. 2016 Oct 20; 167(3):750-762.e14. 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. PMID: 27768894; PMCID: PMC5322940.
      View in: PubMed   Mentions: 218     Fields:    Translation:HumansAnimalsCells
    38. Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A. 2016 08 30; 113(35):9928-33. Wescott MP, Kufareva I, Paes C, Goodman JR, Thaker Y, Puffer BA, Berdougo E, Rucker JB, Handel TM, Doranz BJ. PMID: 27543332; PMCID: PMC5024644.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    39. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol. 2016 10; 30:27-37. Kufareva I. PMID: 27459124; PMCID: PMC5071139.
      View in: PubMed   Mentions: 21     Fields:    Translation:Humans
    40. Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor. Cell Res. 2016 05; 26(5):574-92. Leach K, Gregory KJ, Kufareva I, Khajehali E, Cook AE, Abagyan R, Conigrave AD, Sexton PM, Christopoulos A. PMID: 27002221; PMCID: PMC4856764.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCells
    41. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol. 2016 10; 173(20):2934-51. Ngo T, Kufareva I, Coleman JLj, Graham RM, Abagyan R, Smith NJ. PMID: 26837045; PMCID: PMC5341249.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimals
    42. Disulfide Trapping for Modeling and Structure Determination of Receptor: Chemokine Complexes. Methods Enzymol. 2016; 570:389-420. Kufareva I, Gustavsson M, Holden LG, Qin L, Zheng Y, Handel TM. PMID: 26921956; PMCID: PMC4782801.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    43. Inactivating mutations in GNA13 and RHOA in Burkitt's lymphoma and diffuse large B-cell lymphoma: a tumor suppressor function for the Gα13/RhoA axis in B cells. Oncogene. 2016 07 21; 35(29):3771-80. O'Hayre M, Inoue A, Kufareva I, Wang Z, Mikelis CM, Drummond RA, Avino S, Finkel K, Kalim KW, DiPasquale G, Guo F, Aoki J, Zheng Y, Lionakis MS, Molinolo AA, Gutkind JS. PMID: 26616858; PMCID: PMC4885800.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    44. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. Membranes (Basel). 2015 Oct 23; 5(4):646-63. Lenoir M, Kufareva I, Abagyan R, Overduin M. PMID: 26512702; PMCID: PMC4704004.
      View in: PubMed   Mentions: 20  
    45. Dual targeting of the chemokine receptors CXCR4 and ACKR3 with novel engineered chemokines. J Biol Chem. 2015 Sep 11; 290(37):22385-97. Hanes MS, Salanga CL, Chowdry AB, Comerford I, McColl SR, Kufareva I, Handel TM. PMID: 26216880; PMCID: PMC4566214.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    46. Structure-based predictions of activity cliffs. J Chem Inf Model. 2015 May 26; 55(5):1062-76. Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A. PMID: 25918827; PMCID: PMC4553268.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    47. Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling. Dev Cell. 2015 Apr 20; 33(2):189-203. Lo IC, Gupta V, Midde KK, Taupin V, Lopez-Sanchez I, Kufareva I, Abagyan R, Randazzo PA, Farquhar MG, Ghosh P. PMID: 25865347; PMCID: PMC4415880.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    48. Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies. Immunol Cell Biol. 2015 Apr; 93(4):372-83. Kufareva I, Salanga CL, Handel TM. PMID: 25708536; PMCID: PMC4406842.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansAnimalsCells
    49. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science. 2015 Mar 06; 347(6226):1117-22. Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM. PMID: 25612609; PMCID: PMC4362693.
      View in: PubMed   Mentions: 176     Fields:    Translation:HumansCells
    50. Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs. Methods Mol Biol. 2015; 1335:295-311. Kufareva I, Handel TM, Abagyan R. PMID: 26260608; PMCID: PMC4551442.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    51. Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):E5363-72. Kufareva I, Stephens BS, Holden LG, Qin L, Zhao C, Kawamura T, Abagyan R, Handel TM. PMID: 25468967; PMCID: PMC4273337.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    52. Discovery of novel membrane binding structures and functions. Biochem Cell Biol. 2014 Dec; 92(6):555-63. Kufareva I, Lenoir M, Dancea F, Sridhar P, Raush E, Bissig C, Gruenberg J, Abagyan R, Overduin M. PMID: 25394204; PMCID: PMC4267288.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    53. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell. 2014 Nov 05; 25(22):3654-71. Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P. PMID: 25187647; PMCID: PMC4230624.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansAnimalsCells
    54. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure. 2014 Aug 05; 22(8):1120-1139. Kufareva I, Katritch V, Participants of GPCR Dock 2013, Stevens RC, Abagyan R. PMID: 25066135; PMCID: PMC4126895.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansCells
    55. In silico identification and pharmacological evaluation of novel endocrine disrupting chemicals that act via the ligand-binding domain of the estrogen receptor α. Toxicol Sci. 2014 Sep; 141(1):188-97. McRobb FM, Kufareva I, Abagyan R. PMID: 24928891; PMCID: PMC4271121.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    56. Identification of novel serotonin transporter compounds by virtual screening. J Chem Inf Model. 2014 Mar 24; 54(3):933-43. Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ. PMID: 24521202; PMCID: PMC3982395.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    57. A general method for site specific fluorescent labeling of recombinant chemokines. PLoS One. 2014; 9(1):e81454. Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM. PMID: 24489642; PMCID: PMC3904831.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    58. In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. Environ Sci Technol. 2014; 48(3):1964-72. McRobb FM, Sahagún V, Kufareva I, Abagyan R. PMID: 24392850; PMCID: PMC3951377.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    59. PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):717-23. Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 24406170; PMCID: PMC3975830.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    60. Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5). Theor Biol Med Model. 2013 Sep 14; 10:56. Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW. PMID: 24034446; PMCID: PMC3848485.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    61. Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science. 2013 Sep 20; 341(6152):1387-90. Tan Q, Zhu Y, Li J, Chen Z, Han GW, Kufareva I, Li T, Ma L, Fenalti G, Li J, Zhang W, Xie X, Yang H, Jiang H, Cherezov V, Liu H, Stevens RC, Zhao Q, Wu B. PMID: 24030490; PMCID: PMC3819204.
      View in: PubMed   Mentions: 295     Fields:    Translation:HumansCells
    62. Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone. Biochem J. 2013 Jul 15; 453(2):219-30. Davydov DR, Davydova NY, Sineva EV, Kufareva I, Halpert JR. PMID: 23651100; PMCID: PMC3893034.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    63. Sulfopeptide probes of the CXCR4/CXCL12 interface reveal oligomer-specific contacts and chemokine allostery. ACS Chem Biol. 2013 Sep 20; 8(9):1955-63. Ziarek JJ, Getschman AE, Butler SJ, Taleski D, Stephens B, Kufareva I, Handel TM, Payne RJ, Volkman BF. PMID: 23802178; PMCID: PMC3783652.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    64. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics. Int J Quantum Chem. 2013 Jun 15; 113(12):1669-1675. Ilatovskiy AV, Abagyan R, Kufareva I. PMID: 25414519; PMCID: PMC4235788.
      View in: PubMed   Mentions: 6  
    65. Viral infection controlled by a calcium-dependent lipid-binding module in ALIX. Dev Cell. 2013 May 28; 25(4):364-73. Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J. PMID: 23664863; PMCID: PMC4129370.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansAnimalsCells
    66. The emerging mutational landscape of G proteins and G-protein-coupled receptors in cancer. Nat Rev Cancer. 2013 06; 13(6):412-24. O'Hayre M, Vázquez-Prado J, Kufareva I, Stawiski EW, Handel TM, Seshagiri S, Gutkind JS. PMID: 23640210; PMCID: PMC4068741.
      View in: PubMed   Mentions: 285     Fields:    Translation:HumansAnimalsCells
    67. A structural snapshot of CYP2B4 in complex with paroxetine provides insights into ligand binding and clusters of conformational states. J Pharmacol Exp Ther. 2013 Jul; 346(1):113-20. Shah MB, Kufareva I, Pascual J, Zhang Q, Stout CD, Halpert JR. PMID: 23633618; PMCID: PMC3684837.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    68. Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors. Chem Biol Drug Des. 2013 Jun; 81(6):695-706. Gabrielsen M, Wolosewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. PMID: 23574807; PMCID: PMC3665732.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    69. Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds. PLoS One. 2013; 8(2):e56150. Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K. PMID: 23437089; PMCID: PMC3577790.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    70. A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer. Methods Mol Biol. 2013; 1013:93-127. Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM. PMID: 23625495; PMCID: PMC4091634.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    71. Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases. Annu Rev Pharmacol Toxicol. 2013; 53:331-54. Montaner S, Kufareva I, Abagyan R, Gutkind JS. PMID: 23092247; PMCID: PMC4074518.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    72. Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies. J Med Chem. 2012 Apr 12; 55(7):3049-57. Sager G, Ørvoll EØ, Lysaa RA, Kufareva I, Abagyan R, Ravna AW. PMID: 22380603; PMCID: PMC4181661.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    73. Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors. Eur J Med Chem. 2012 Mar; 49:200-10. Jaronczyk M, Wolosewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z. PMID: 22309909; PMCID: PMC3365592.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    74. Compound activity prediction using models of binding pockets or ligand properties in 3D. Curr Top Med Chem. 2012; 12(17):1869-82. Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R. PMID: 23116466; PMCID: PMC4085113.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    75. Methods of protein structure comparison. Methods Mol Biol. 2012; 857:231-57. Kufareva I, Abagyan R. PMID: 22323224; PMCID: PMC4321859.
      View in: PubMed   Mentions: 152     Fields:    Translation:Cells
    76. Pocketome: an encyclopedia of small-molecule binding sites in 4D. Nucleic Acids Res. 2012 Jan; 40(Database issue):D535-40. Kufareva I, Ilatovskiy AV, Abagyan R. PMID: 22080553; PMCID: PMC3245087.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    77. Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol. Eur J Med Chem. 2012 Jan; 47(1):24-37. Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I. PMID: 22071255; PMCID: PMC3357065.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    78. Tyrosine phosphorylation of the Gα-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration. Sci Signal. 2011 Sep 27; 4(192):ra64. Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P. PMID: 21954290; PMCID: PMC4226136.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    79. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure. 2011 Aug 10; 19(8):1108-26. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R, GPCR Dock 2010 participants. PMID: 21827947; PMCID: PMC3154726.
      View in: PubMed   Mentions: 115     Fields:    Translation:HumansCells
    80. Structure based prediction of subtype-selectivity for adenosine receptor antagonists. Neuropharmacology. 2011 Jan; 60(1):108-15. Katritch V, Kufareva I, Abagyan R. PMID: 20637786; PMCID: PMC2980563.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    81. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des. 2010 May; 24(5):459-71. Park SJ, Kufareva I, Abagyan R. PMID: 20455005; PMCID: PMC2881208.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    82. Spatial chemical distance based on atomic property fields. J Comput Aided Mol Des. 2010 Mar; 24(3):173-82. Grigoryan AV, Kufareva I, Totrov M, Abagyan RA. PMID: 20229197; PMCID: PMC2858276.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    83. Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists. J Med Chem. 2010 Feb 25; 53(4):1799-809. Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R. PMID: 20095623; PMCID: PMC2826142.
      View in: PubMed   Mentions: 97     Fields:    Translation:HumansAnimalsCells
    84. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem. 2009 Jan 22; 52(2):397-406. Bottegoni G, Kufareva I, Totrov M, Abagyan R. PMID: 19090659; PMCID: PMC2662720.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    85. The flexible pocketome engine for structural chemogenomics. Methods Mol Biol. 2009; 575:249-79. Abagyan R, Kufareva I. PMID: 19727619; PMCID: PMC2975493.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    86. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem. 2008 Dec 25; 51(24):7921-32. Kufareva I, Abagyan R. PMID: 19053777; PMCID: PMC2669721.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    87. Optimization of high throughput virtual screening by combining shape-matching and docking methods. J Chem Inf Model. 2008 Mar; 48(3):489-97. Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S. PMID: 18302357.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    88. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J Comput Aided Mol Des. 2008 May; 22(5):311-25. Bottegoni G, Kufareva I, Totrov M, Abagyan R. PMID: 18273556; PMCID: PMC2641994.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    89. 3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A. 2007 Nov 20; 104(47):18619-24. Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E. PMID: 18003900; PMCID: PMC2141826.
      View in: PubMed   Mentions: 77     Fields:    Translation:HumansAnimalsCells
    90. Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science. 2007 Jul 27; 317(5837):516-9. Outeiro TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, Amore AM, Volk CB, Maxwell MM, Rochet JC, McLean PJ, Young AB, Abagyan R, Feany MB, Hyman BT, Kazantsev AG. PMID: 17588900.
      View in: PubMed   Mentions: 477     Fields:    Translation:HumansAnimalsCells
    91. PIER: protein interface recognition for structural proteomics. Proteins. 2007 May 01; 67(2):400-17. Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. PMID: 17299750.
      View in: PubMed   Mentions: 49     Fields:    Translation:Cells
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