Soo-Kyung Kim - Publications

Affiliations: 
California Institute of Technology, Pasadena, CA 

73 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kim SK, Suebka S, Gin A, Nguyen PD, Tang Y, Su J, Goddard WA. Methotrexate Inhibits the Binding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor Binding Domain to the Host-Cell Angiotensin-Converting Enzyme-2 (ACE-2) Receptor. Acs Pharmacology & Translational Science. 7: 348-362. PMID 38357278 DOI: 10.1021/acsptsci.3c00197  0.345
2023 Vo AP, Kim SK, Yang MY, Ondrus AE, Goddard WA. Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex. Proceedings of the National Academy of Sciences of the United States of America. 120: e2300919120. PMID 38015850 DOI: 10.1073/pnas.2300919120  0.331
2023 Ko B, Jang Y, Kwak SH, You H, Kim JH, Lee JE, Park HD, Kim SK, Goddard WA, Han JH, Kim YC. Discovery of 3-Phenyl Indazole-Based Novel Chemokine-like Receptor 1 Antagonists for the Treatment of Psoriasis. Journal of Medicinal Chemistry. PMID 37883692 DOI: 10.1021/acs.jmedchem.3c01011  0.538
2023 Li B, Maruszko K, Kim SK, Yang MY, Vo AP, Goddard WA. Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist. Journal of the American Chemical Society. PMID 37672637 DOI: 10.1021/jacs.3c05996  0.384
2023 Mafi A, Kim SK, Goddard WA. The dynamics of agonist-β-adrenergic receptor activation induced by binding of GDP-bound Gs protein. Nature Chemistry. PMID 37349378 DOI: 10.1038/s41557-023-01238-6  0.387
2023 Tokmakova A, Kim D, Guthrie B, Kim SK, Goddard WA, Liggett SB. Predicted structure and cell signaling of TAS2R14 reveal receptor hyper-flexibility for detecting diverse bitter tastes. Iscience. 26: 106422. PMID 37096045 DOI: 10.1016/j.isci.2023.106422  0.523
2023 Jung JH, Jang IH, Yang MY, Kim S, Kim SK, Goddard WA, Kim YC. Discovery and Binding Mechanism of Pyrazoloisoquinoline-Based Novel β-Arrestin Inverse Agonists of the Kappa-Opioid Receptor. Journal of Medicinal Chemistry. PMID 36987735 DOI: 10.1021/acs.jmedchem.3c00064  0.591
2023 Hernández PM, Arango CA, Kim SK, Jaramillo-Botero A, Goddard WA. Predicted Three-Dimensional Structure of the GCR1 Putative GPCR in and Its Binding to Abscisic Acid and Gibberellin A1. Journal of Agricultural and Food Chemistry. PMID 36977192 DOI: 10.1021/acs.jafc.2c06846  0.34
2023 Wang X, Neale C, Kim SK, Goddard WA, Ye L. Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery. Nature Communications. 14: 1325. PMID 36899002 DOI: 10.1038/s41467-023-36971-6  0.379
2022 Yang MY, Kim SK, Goddard WA. G protein coupling and activation of the metabotropic GABA heterodimer. Nature Communications. 13: 4612. PMID 35941188 DOI: 10.1038/s41467-022-32213-3  0.368
2022 Jacobson KA, Kim HS, Ravi G, Kim SK, Lee K, Chen A, Chen W, Kim SG, Barak D, Liang BT, Gao ZG. Engineering of A Adenosine and P2Y Nucleotide Receptors and Their Ligands. Drug Development Research. 58: 330-339. PMID 35799977 DOI: 10.1002/ddr.10168  0.819
2022 Mafi A, Kim SK, Goddard WA. The mechanism for ligand activation of the GPCR-G protein complex. Proceedings of the National Academy of Sciences of the United States of America. 119: e2110085119. PMID 35452328 DOI: 10.1073/pnas.2110085119  0.317
2021 Mafi A, Kim SK, Goddard WA. The G protein-first activation mechanism of opioid receptors by Gi protein and agonists. Qrb Discovery. 2: e9. PMID 37529677 DOI: 10.1017/qrd.2021.7  0.378
2021 Yang MY, Mafi A, Kim SK, Goddard WA, Guthrie B. Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists. Qrb Discovery. 2: e3. PMID 37529671 DOI: 10.1017/qrd.2021.1  0.495
2021 Yang MY, Mafi A, Kim SK, Goddard WA, Guthrie B. Predicted structure of fully activated human bitter taste receptor TAS2R4 complexed with G protein and agonists. Qrb Discovery. 2: e3. PMID 37529671 DOI: 10.1017/qrd.2021.1  0.495
2021 Jang J, Kim SK, Guthrie B, Goddard WA. Synergic Effects in the Activation of the Sweet Receptor GPCR Heterodimer for Various Sweeteners Predicted Using Molecular Metadynamics Simulations. Journal of Agricultural and Food Chemistry. PMID 34613740 DOI: 10.1021/acs.jafc.1c03779  0.318
2021 Mafi A, Kim SK, Chou KC, Güthrie B, Goddard WA. Predicted Structure of Fully Activated Tas1R3/1R3' Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars. Journal of the American Chemical Society. PMID 34585929 DOI: 10.1021/jacs.1c08839  0.313
2021 Yang MY, Kim SK, Kim D, Liggett SB, Goddard WA. Structures and Agonist Binding Sites of Bitter Taste Receptor TAS2R5 Complexed with Gi Protein and Validated against Experiment. The Journal of Physical Chemistry Letters. 9293-9300. PMID 34542294 DOI: 10.1021/acs.jpclett.1c02162  0.52
2020 Mafi A, Kim SK, Goddard WA. Mechanism of β-arrestin recruitment by the μ-opioid G protein-coupled receptor. Proceedings of the National Academy of Sciences of the United States of America. PMID 32601232 DOI: 10.1073/Pnas.1918264117  0.408
2020 Mafi A, Kim SK, Goddard WA. The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist. Proceedings of the National Academy of Sciences of the United States of America. PMID 32127473 DOI: 10.1073/Pnas.1910006117  0.478
2020 Sharma VK, Xuyu Y, Sanchez D, Kim S, Goddard WA, Loh YP. Extracellular interaction between Neurotrophic factor‐α1 and HTR1E serotonin receptor promotes cell survival The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.01952  0.44
2019 Jeong P, Kim SK, Li Q, Oh SJ, Son S, Chen G, Tan H, Kim S, Park JH, Park KD, Kim YO, Yoon MH, Kim YC, Goddard W. Discovery of Novel Biased Opioid Receptor Ligands through Structure-Based Pharmacophore Virtual Screening and Experiment. Chemmedchem. PMID 31359587 DOI: 10.1002/Cmdc.201900418  0.619
2017 Shankar V, Goddard WA, Kim SK, Abrol R. The Predicted 3D Structure of Human DP Prostaglandin G Protein-Coupled Receptor Bound to CPI Antagonist. Journal of Chemical Theory and Computation. PMID 29268008 DOI: 10.1021/Acs.Jctc.7B00842  0.568
2017 Kim SK, Chen Y, Abrol R, Goddard WA, Guthrie B. Activation mechanism of the G protein-coupled sweet receptor heterodimer with sweeteners and allosteric agonists. Proceedings of the National Academy of Sciences of the United States of America. PMID 28228527 DOI: 10.1073/Pnas.1700001114  0.565
2016 Kim JH, Kim SK, Lee JH, Kim YJ, Goddard WA, Kim YC. Homology modeling and molecular docking studies of Drosophila and Aedes sex peptide receptors. Journal of Molecular Graphics & Modelling. 66: 115-122. PMID 27060892 DOI: 10.1016/J.Jmgm.2016.03.014  0.668
2015 de March CA, Kim SK, Antonczak S, Goddard WA, Golebiowski J. G protein-coupled odorant receptors: From sequence to structure. Protein Science : a Publication of the Protein Society. PMID 26044705 DOI: 10.1002/Pro.2717  0.486
2015 Li Q, Kim SK, Goddard WA, Chen G, Tan H. Predicted structures for kappa opioid G-protein coupled receptor bound to selective agonists. Journal of Chemical Information and Modeling. 55: 614-27. PMID 25642595 DOI: 10.1021/Ci500523Z  0.574
2014 Kim SK, Goddard WA. Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1. Journal of Computer-Aided Molecular Design. 28: 1175-90. PMID 25224127 DOI: 10.1007/S10822-014-9793-4  0.48
2014 Kim SK, Goddard WA, Yi KY, Lee BH, Lim CJ, Trzaskowski B. Predicted ligands for the human urotensin-II G protein-coupled receptor with some experimental validation. Chemmedchem. 9: 1732-43. PMID 24989481 DOI: 10.1002/Cmdc.201402087  0.457
2013 Abrol R, Kim SK, Bray JK, Trzaskowski B, Goddard WA. Conformational ensemble view of G protein-coupled receptors and the effect of mutations and ligand binding. Methods in Enzymology. 520: 31-48. PMID 23332694 DOI: 10.1016/B978-0-12-391861-1.00002-2  0.574
2012 Charlier L, Topin J, Ronin C, Kim SK, Goddard WA, Efremov R, Golebiowski J. How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case. Cellular and Molecular Life Sciences : Cmls. 69: 4205-13. PMID 22926438 DOI: 10.1007/S00018-012-1116-0  0.553
2011 Abrol R, Kim SK, Bray JK, Griffith AR, Goddard WA. Characterizing and predicting the functional and conformational diversity of seven-transmembrane proteins. Methods (San Diego, Calif.). 55: 405-14. PMID 22197575 DOI: 10.1016/J.Ymeth.2011.12.005  0.52
2011 Kim SK, Fristrup P, Abrol R, Goddard WA. Structure-based prediction of subtype selectivity of histamine H 3 receptor selective antagonists in clinical trials Journal of Chemical Information and Modeling. 51: 3262-3274. PMID 22035233 DOI: 10.1021/Ci200435B  0.499
2011 Kim SK, Riley L, Abrol R, Jacobson KA, Goddard WA. Predicted structures of agonist and antagonist bound complexes of adenosine A3 receptor. Proteins. 79: 1878-97. PMID 21488099 DOI: 10.1002/Prot.23012  0.664
2011 Kim SK, Li Y, Abrol R, Heo J, Goddard WA. Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors. Journal of Chemical Information and Modeling. 51: 420-33. PMID 21299232 DOI: 10.1021/Ci100375B  0.536
2010 Kim SK, Li Y, Park C, Abrol R, Goddard WA. Prediction of the three-dimensional structure for the rat urotensin II receptor, and comparison of the antagonist binding sites and binding selectivity between human and rat receptors from atomistic simulations. Chemmedchem. 5: 1594-608. PMID 20683923 DOI: 10.1002/Cmdc.201000175  0.515
2010 Goddard WA, Kim SK, Li Y, Trzaskowski B, Griffith AR, Abrol R. Predicted 3D structures for adenosine receptors bound to ligands: comparison to the crystal structure. Journal of Structural Biology. 170: 10-20. PMID 20079848 DOI: 10.1016/J.Jsb.2010.01.001  0.49
2009 Gallagher DT, Smith N, Kim SK, Robinson H, Reddy PT. Profound asymmetry in the structure of the cAMP-free cAMP Receptor Protein (CRP) from Mycobacterium tuberculosis. The Journal of Biological Chemistry. 284: 8228-32. PMID 19193643 DOI: 10.1074/Jbc.C800215200  0.426
2008 Wess J, Han SJ, Kim SK, Jacobson KA, Li JH. Conformational changes involved in G-protein-coupled-receptor activation. Trends in Pharmacological Sciences. 29: 616-25. PMID 18838178 DOI: 10.1016/J.Tips.2008.08.006  0.649
2008 Melman A, Wang B, Joshi BV, Gao ZG, Castro Sd, Heller CL, Kim SK, Jeong LS, Jacobson KA. Selective A(3) adenosine receptor antagonists derived from nucleosides containing a bicyclo[3.1.0]hexane ring system. Bioorganic & Medicinal Chemistry. 16: 8546-56. PMID 18752961 DOI: 10.1016/J.Bmc.2008.08.007  0.815
2008 Li JH, Hamdan FF, Kim SK, Jacobson KA, Zhang X, Han SJ, Wess J. Ligand-specific changes in M3 muscarinic acetylcholine receptor structure detected by a disulfide scanning strategy. Biochemistry. 47: 2776-88. PMID 18247581 DOI: 10.1021/Bi7019113  0.682
2007 Li JH, Han SJ, Hamdan FF, Kim SK, Jacobson KA, Bloodworth LM, Zhang X, Wess J. Distinct structural changes in a G protein-coupled receptor caused by different classes of agonist ligands. The Journal of Biological Chemistry. 282: 26284-93. PMID 17623649 DOI: 10.1074/Jbc.M704875200  0.705
2007 Scarselli M, Li B, Kim SK, Wess J. Multiple residues in the second extracellular loop are critical for M3 muscarinic acetylcholine receptor activation. The Journal of Biological Chemistry. 282: 7385-96. PMID 17213190 DOI: 10.1074/Jbc.M610394200  0.524
2007 Li B, Scarselli M, Knudsen CD, Kim SK, Jacobson KA, McMillin SM, Wess J. Rapid identification of functionally critical amino acids in a G protein-coupled receptor. Nature Methods. 4: 169-74. PMID 17206152 DOI: 10.1038/Nmeth990  0.586
2007 Li JH, Han S, Hamdan FF, Kim S, Jacobson KA, Bloodworth LM, Zhang X, Wess J. Identification of distinct, ligand‐specific structural changes in a G protein‐coupled receptor The Faseb Journal. 21. DOI: 10.1096/Fasebj.21.5.A425-C  0.597
2006 Cosyn L, Palaniappan KK, Kim SK, Duong HT, Gao ZG, Jacobson KA, Van Calenbergh S. 2-triazole-substituted adenosines: a new class of selective A3 adenosine receptor agonists, partial agonists, and antagonists. Journal of Medicinal Chemistry. 49: 7373-83. PMID 17149867 DOI: 10.1021/Jm0608208  0.697
2006 Jacobson KA, Costanzi S, Kim SK, Roh E, Joshi BV, Tchilibon S, Duong HT, Gao ZG. Action of nucleosides and nucleotides at 7 transmembrane-spanning receptors. Nucleosides, Nucleotides & Nucleic Acids. 25: 1425-36. PMID 17067963 DOI: 10.1080/15257770600919027  0.843
2006 Kim SK, Gao ZG, Jeong LS, Jacobson KA. Docking studies of agonists and antagonists suggest an activation pathway of the A3 adenosine receptor. Journal of Molecular Graphics & Modelling. 25: 562-77. PMID 16793299 DOI: 10.1016/J.Jmgm.2006.05.004  0.731
2006 Kim SK, Jacobson KA. Computational prediction of homodimerization of the A3 adenosine receptor. Journal of Molecular Graphics & Modelling. 25: 549-61. PMID 16781879 DOI: 10.1016/J.Jmgm.2006.03.003  0.566
2006 Gao ZG, Duong HT, Sonina T, Kim SK, Van Rompaey P, Van Calenbergh S, Mamedova L, Kim HO, Kim MJ, Kim AY, Liang BT, Jeong LS, Jacobson KA. Orthogonal activation of the reengineered A3 adenosine receptor (neoceptor) using tailored nucleoside agonists. Journal of Medicinal Chemistry. 49: 2689-702. PMID 16640329 DOI: 10.1021/Jm050968B  0.831
2006 Gao ZG, Joshi BV, Klutz AM, Kim SK, Lee HW, Kim HO, Jeong LS, Jacobson KA. Conversion of A3 adenosine receptor agonists into selective antagonists by modification of the 5'-ribofuran-uronamide moiety. Bioorganic & Medicinal Chemistry Letters. 16: 596-601. PMID 16289820 DOI: 10.1016/J.Bmcl.2005.10.054  0.662
2006 Gao Z, Joshi BV, Klutz AM, Kim S, Lee HW, Kim HO, Jeong LS, Jacobson KA. Conversion of A3 Adenosine Receptor Agonists into Selective Antagonists by Modification of the 5′-Ribofuran-uronamide Moiety. Cheminform. 37. DOI: 10.1002/CHIN.200618207  0.643
2005 Han SJ, Hamdan FF, Kim SK, Jacobson KA, Bloodworth LM, Li B, Wess J. Identification of an agonist-induced conformational change occurring adjacent to the ligand-binding pocket of the M(3) muscarinic acetylcholine receptor. The Journal of Biological Chemistry. 280: 34849-58. PMID 16093246 DOI: 10.1074/Jbc.M506711200  0.705
2005 Gao ZG, Kim SK, Ijzerman AP, Jacobson KA. Allosteric modulation of the adenosine family of receptors. Mini Reviews in Medicinal Chemistry. 5: 545-53. PMID 15974932 DOI: 10.2174/1389557054023242  0.676
2005 Han SJ, Hamdan FF, Kim SK, Jacobson KA, Brichta L, Bloodworth LM, Li JH, Wess J. Pronounced conformational changes following agonist activation of the M(3) muscarinic acetylcholine receptor. The Journal of Biological Chemistry. 280: 24870-9. PMID 15870064 DOI: 10.1074/Jbc.M500379200  0.676
2005 Tchilibon S, Joshi BV, Kim SK, Duong HT, Gao ZG, Jacobson KA. (N)-methanocarba 2,N6-disubstituted adenine nucleosides as highly potent and selective A3 adenosine receptor agonists. Journal of Medicinal Chemistry. 48: 1745-58. PMID 15771421 DOI: 10.1021/Jm049580R  0.636
2005 Jacobson KA, Ohno M, Duong HT, Kim SK, Tchilibon S, Cesnek M, Holý A, Gao ZG. A neoceptor approach to unraveling microscopic interactions between the human A2A adenosine receptor and its agonists. Chemistry & Biology. 12: 237-47. PMID 15734651 DOI: 10.1016/J.Chembiol.2004.12.010  0.679
2005 Lou H, Kim SK, Zaitsev E, Snell CR, Lu B, Loh YP. Sorting and activity-dependent secretion of BDNF require interaction of a specific motif with the sorting receptor carboxypeptidase E Neuron. 45: 245-255. PMID 15664176 DOI: 10.1016/J.Neuron.2004.12.037  0.411
2005 Li B, Nowak NM, Kim SK, Jacobson KA, Bagheri A, Schmidt C, Wess J. Random mutagenesis of the M3 muscarinic acetylcholine receptor expressed in yeast: identification of second-site mutations that restore function to a coupling-deficient mutant M3 receptor. The Journal of Biological Chemistry. 280: 5664-75. PMID 15572356 DOI: 10.1074/Jbc.M411623200  0.658
2004 Jacobson KA, Kim SK, Costanzi S, Gao ZG. Purine receptors: GPCR structure and agonist design. Molecular Interventions. 4: 337-47. PMID 15616163 DOI: 10.1124/Mi.4.6.7  0.809
2004 Jeong LS, Kim MJ, Kim HO, Gao ZG, Kim SK, Jacobson KA, Chun MW. Design and synthesis of 3'-ureidoadenosine-5'-uronamides: effects of the 3'-ureido group on binding to the A3 adenosine receptor. Bioorganic & Medicinal Chemistry Letters. 14: 4851-4. PMID 15341938 DOI: 10.1016/J.Bmcl.2004.07.042  0.652
2004 Ohno M, Gao ZG, Van Rompaey P, Tchilibon S, Kim SK, Harris BA, Gross AS, Duong HT, Van Calenbergh S, Jacobson KA. Modulation of adenosine receptor affinity and intrinsic efficacy in adenine nucleosides substituted at the 2-position. Bioorganic & Medicinal Chemistry. 12: 2995-3007. PMID 15142558 DOI: 10.1016/J.Bmc.2004.03.031  0.707
2004 Tchilibon S, Kim SK, Gao ZG, Harris BA, Blaustein JB, Gross AS, Duong HT, Melman N, Jacobson KA. Exploring distal regions of the A3 adenosine receptor binding site: sterically constrained N6-(2-phenylethyl)adenosine derivatives as potent ligands. Bioorganic & Medicinal Chemistry. 12: 2021-34. PMID 15080906 DOI: 10.1016/J.Bmc.2004.02.037  0.688
2004 Jung KY, Kim SK, Gao ZG, Gross AS, Melman N, Jacobson KA, Kim YC. Structure-activity relationships of thiazole and thiadiazole derivatives as potent and selective human adenosine A3 receptor antagonists. Bioorganic & Medicinal Chemistry. 12: 613-23. PMID 14738972 DOI: 10.1016/J.Bmc.2003.10.041  0.776
2003 Moro S, Deflorian F, Spalluto G, Pastorin G, Cacciari B, Kim SK, Jacobson KA. Demystifying the three dimensional structure of G protein-coupled receptors (GPCRs) with the aid of molecular modeling. Chemical Communications (Cambridge, England). 2949-56. PMID 14703805 DOI: 10.1039/B303439A  0.761
2003 Kim SK, Gao ZG, Van Rompaey P, Gross AS, Chen A, Van Calenbergh S, Jacobson KA. Modeling the adenosine receptors: comparison of the binding domains of A2A agonists and antagonists. Journal of Medicinal Chemistry. 46: 4847-59. PMID 14584936 DOI: 10.1021/Jm0300431  0.663
2003 Lee S, Yi KY, Kim SK, Suh J, Kim NJ, Yoo SE, Lee BH, Seo HW, Kim SO, Lim H. Cardioselective anti-ischemic ATP-sensitive potassium channel (KATP) openers: benzopyranyl indoline and indole analogues. European Journal of Medicinal Chemistry. 38: 459-71. PMID 12767596 DOI: 10.1016/S0223-5234(03)00063-1  0.309
2003 Gao ZG, Kim SK, Gross AS, Chen A, Blaustein JB, Jacobson KA. Identification of essential residues involved in the allosteric modulation of the human A(3) adenosine receptor. Molecular Pharmacology. 63: 1021-31. PMID 12695530 DOI: 10.1124/Mol.63.5.1021  0.677
2003 Jacobson KA, Kim HS, Ravi G, Kim S, Lee K, Chen A, Chen W, Kim SG, Barak D, Liang BT, Gao Z. Engineering of A3 adenosine and P2Y nucleotide receptors and their ligands Drug Development Research. 58: 330-339. DOI: 10.1002/Ddr.10168  0.828
2002 Gao ZG, Kim SK, Biadatti T, Chen W, Lee K, Barak D, Kim SG, Johnson CR, Jacobson KA. Structural determinants of A(3) adenosine receptor activation: nucleoside ligands at the agonist/antagonist boundary. Journal of Medicinal Chemistry. 45: 4471-84. PMID 12238926 DOI: 10.1021/jm020211  0.818
2002 Gao ZG, Chen A, Barak D, Kim SK, Müller CE, Jacobson KA. Identification by site-directed mutagenesis of residues involved in ligand recognition and activation of the human A3 adenosine receptor. The Journal of Biological Chemistry. 277: 19056-63. PMID 11891221 DOI: 10.1074/Jbc.M110960200  0.75
1999 Yoo S, Kim S, Lee S, Yi KY, Lee D. A comparative molecular field analysis and molecular modelling studies on pyridylimidazole type of angiotensin II antagonists. Bioorganic & Medicinal Chemistry. 7: 2971-2976. PMID 10658603 DOI: 10.1016/S0968-0896(99)00245-X  0.425
1997 Yoo S, Lee S, Kim S, Lee S. The conformation and activity relationship of benzofuran derivatives as angiotensin II receptor antagonists Bioorganic & Medicinal Chemistry. 5: 445-459. PMID 9061209 DOI: 10.1016/S0968-0896(96)00244-1  0.523
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