Ruben Abagyan

Ruben Abagyan

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Ruben Abagyan

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Unique metabolite preferences of the drug transporters OAT1 and OAT3 analyzed by machine learning.

J Biol Chem 2020 Feb 2;295(7):1829-1842. Epub 2020 Jan 2.

Department of Pediatrics, University of California San Diego, La Jolla, California 92093-0693

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http://dx.doi.org/10.1074/jbc.RA119.010729DOI Listing
February 2020

Druggable exosites of the human kino-pocketome.

J Comput Aided Mol Des 2020 Jan 10. Epub 2020 Jan 10.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA.

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http://dx.doi.org/10.1007/s10822-019-00276-yDOI Listing
January 2020

Identification of Four Amoebicidal Nontoxic Compounds by a Molecular Docking Screen of Sterol Δ8-Δ7-Isomerase and Phenotypic Assays.

ACS Infect Dis 2019 Dec 17;5(12):2029-2038. Epub 2019 Oct 17.

Skaggs School of Pharmacy and Pharmaceutical Science , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States.

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http://dx.doi.org/10.1021/acsinfecdis.9b00227DOI Listing
December 2019

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4.

J Comput Aided Mol Des 2019 Dec 9;33(12):1057-1069. Epub 2019 Oct 9.

Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, CA, 92121, USA.

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http://dx.doi.org/10.1007/s10822-019-00225-9DOI Listing
December 2019

Proton-pump inhibitor use is associated with a broad spectrum of neurological adverse events including impaired hearing, vision, and memory.

Sci Rep 2019 Nov 21;9(1):17280. Epub 2019 Nov 21.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41598-019-53622-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872761PMC
November 2019

Multi-center screening of the Pathogen Box collection for schistosomiasis drug discovery.

Parasit Vectors 2019 Oct 22;12(1):493. Epub 2019 Oct 22.

Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/s13071-019-3747-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805474PMC
October 2019

Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant.

ACS Omega 2019 Oct 2;4(16):16999-17008. Epub 2019 Oct 2.

Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry and Biochemistry, and School of Medicine, University of California San Diego, La Jolla, California 92093, United States.

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http://dx.doi.org/10.1021/acsomega.9b02491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796237PMC
October 2019

Nilotinib, an approved leukemia drug, inhibits smoothened signaling in Hedgehog-dependent medulloblastoma.

PLoS One 2019 20;14(9):e0214901. Epub 2019 Sep 20.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego (UCSD), La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214901PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754133PMC
September 2019

Retrospective analysis reveals significant association of hypoglycemia with tramadol and methadone in contrast to other opioids.

Sci Rep 2019 Aug 28;9(1):12490. Epub 2019 Aug 28.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41598-019-48955-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713717PMC
August 2019

Extended Multitarget Pharmacology of Anticancer Drugs.

J Chem Inf Model 2019 Jun 3;59(6):3006-3017. Epub 2019 May 3.

Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093-0747 , United States.

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http://dx.doi.org/10.1021/acs.jcim.9b00031DOI Listing
June 2019

Population Scale Retrospective Analysis Reveals Potential Risk of Cholestasis in Pregnant Women Taking Omeprazole, Lansoprazole, and Amoxicillin.

Interdiscip Sci 2019 Jun 20;11(2):273-281. Epub 2019 May 20.

Medicine Engineering Research Center, College of Pharmacy, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.

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http://dx.doi.org/10.1007/s12539-019-00335-wDOI Listing
June 2019

Molecular Basis of Action of a Small-Molecule Positive Allosteric Modulator Agonist at the Type 1 Cholecystokinin Holoreceptor.

Mol Pharmacol 2019 03 27;95(3):245-259. Epub 2018 Dec 27.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (A.J.D., L.J.M.); In Silico Drug Discovery Department, Icagen Tucson Innovation Center, Oro Valley, Arizona (I.M., K.N., A.N.); Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Australia (C.V., D.W., P.M.S., A.C., L.J.M.); Molsoft, La Jolla, California (P.C.H.L., A.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and School of Pharmacy, Fudan University, Shanghai, China (D.W., P.M.S.)

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http://dx.doi.org/10.1124/mol.118.114082DOI Listing
March 2019

2-Aminothiazole Derivatives as Selective Allosteric Modulators of the Protein Kinase CK2. 1. Identification of an Allosteric Binding Site.

J Med Chem 2019 02 18;62(4):1803-1816. Epub 2019 Feb 18.

Université de Lyon, Université Lyon 1, Faculté de Pharmacie, ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, F-69373 , Lyon Cedex 08, France.

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http://dx.doi.org/10.1021/acs.jmedchem.8b01766DOI Listing
February 2019

Analysis of postmarketing safety data for proton-pump inhibitors reveals increased propensity for renal injury, electrolyte abnormalities, and nephrolithiasis.

Sci Rep 2019 Feb 19;9(1):2282. Epub 2019 Feb 19.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093-0747, USA.

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http://www.nature.com/articles/s41598-019-39335-7
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http://dx.doi.org/10.1038/s41598-019-39335-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381091PMC
February 2019

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3.

J Comput Aided Mol Des 2019 01 9;33(1):35-46. Epub 2018 Aug 9.

Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, CA, 92121, USA.

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http://dx.doi.org/10.1007/s10822-018-0139-5DOI Listing
January 2019

In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase.

Mol Microbiol 2018 10 2;110(1):128-142. Epub 2018 Oct 2.

Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.

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http://dx.doi.org/10.1111/mmi.14093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595482PMC
October 2018

Protein-RNA Docking Using ICM.

J Chem Theory Comput 2018 Sep 9;14(9):4971-4984. Epub 2018 Aug 9.

Molsoft L.L.C., 11199 Sorrento Valley Road, S209 , San Diego , California 92121 , United States.

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b00293
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http://dx.doi.org/10.1021/acs.jctc.8b00293DOI Listing
September 2018

Dexamethasone and Fludrocortisone Inhibit Hedgehog Signaling in Embryonic Cells.

ACS Omega 2018 Sep 26;3(9):12019-12025. Epub 2018 Sep 26.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92037, United States.

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http://dx.doi.org/10.1021/acsomega.8b01864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6645496PMC
September 2018

Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia.

Am J Psychiatry 2018 07 2;175(7):674-682. Epub 2018 Mar 2.

From the Center for Multimodal Imaging and Genetics, the Department of Radiology, the Center for Computational Biology and Bioinformatics, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, Calif.; the Department of Radiation Sciences, Umeå University, Umeå, Sweden; and NORMENT, KG Jebsen Center for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo.

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http://dx.doi.org/10.1176/appi.ajp.2017.17040410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028303PMC
July 2018

Population scale retrospective analysis reveals distinctive antidepressant and anxiolytic effects of diclofenac, ketoprofen and naproxen in patients with pain.

PLoS One 2018 18;13(4):e0195521. Epub 2018 Apr 18.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195521PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905979PMC
July 2018

Hedgehog pathway and smoothened inhibitors in cancer therapies.

Anticancer Drugs 2018 06;29(5):387-401

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1097/CAD.0000000000000609DOI Listing
June 2018

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.

J Comput Aided Mol Des 2018 01 8;32(1):187-198. Epub 2017 Sep 8.

Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, CA, 92121, USA.

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http://dx.doi.org/10.1007/s10822-017-0058-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767200PMC
January 2018

Publisher Correction: Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications.

Sci Rep 2017 12 5;7(1):17268. Epub 2017 Dec 5.

School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.

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http://www.nature.com/articles/s41598-017-14992-8
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http://dx.doi.org/10.1038/s41598-017-14992-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717077PMC
December 2017

Multi-targeting Drug Community Challenge.

Cell Chem Biol 2017 12;24(12):1434-1435

Department of Cell, Developmental and Regenerative Biology and School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2017.12.006DOI Listing
December 2017

CYP51 is an essential drug target for the treatment of primary amoebic meningoencephalitis (PAM).

PLoS Negl Trop Dis 2017 12 28;11(12):e0006104. Epub 2017 Dec 28.

Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0006104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746216PMC
December 2017

Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor.

Nucleic Acids Res 2017 Sep;45(15):8835-8843

The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.

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http://dx.doi.org/10.1093/nar/gkx523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587751PMC
September 2017

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens.

PeerJ 2017 19;5:e3765. Epub 2017 Sep 19.

Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, CA, United States of America.

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http://dx.doi.org/10.7717/peerj.3765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609521PMC
September 2017

Inhibition of PDE5A1 guanosine cyclic monophosphate (cGMP) hydrolysing activity by sildenafil analogues that inhibit cellular cGMP efflux.

J Pharm Pharmacol 2017 Jun 17;69(6):675-683. Epub 2017 Feb 17.

Experimental and Clinical Pharmacology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway.

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http://dx.doi.org/10.1111/jphp.12693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434896PMC
June 2017

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

Immunity 2017 06;46(6):1005-1017.e5

University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572563PMC
June 2017

Population scale data reveals the antidepressant effects of ketamine and other therapeutics approved for non-psychiatric indications.

Sci Rep 2017 05 3;7(1):1450. Epub 2017 May 3.

School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1038/s41598-017-01590-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5431207PMC
May 2017

A Thiazole Orange Derivative Targeting the Bacterial Protein FtsZ Shows Potent Antibacterial Activity.

Front Microbiol 2017 11;8:855. Epub 2017 May 11.

Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic UniversityHong Kong, Hong Kong.

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http://dx.doi.org/10.3389/fmicb.2017.00855DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5426085PMC
May 2017

Orphan receptor ligand discovery by pickpocketing pharmacological neighbors.

Nat Chem Biol 2017 02 19;13(2):235-242. Epub 2016 Dec 19.

Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.

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http://dx.doi.org/10.1038/nchembio.2266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5247308PMC
February 2017

Structural basis of ligand interaction with atypical chemokine receptor 3.

Nat Commun 2017 01 18;8:14135. Epub 2017 Jan 18.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, MC 0684, La Jolla, California, 92093, USA.

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http://dx.doi.org/10.1038/ncomms14135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253664PMC
January 2017

Identifying ligands at orphan GPCRs: current status using structure-based approaches.

Br J Pharmacol 2016 10 5;173(20):2934-51. Epub 2016 Mar 5.

Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.

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http://dx.doi.org/10.1111/bph.13452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5341249PMC
October 2016

Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.

J Pharmacol Exp Ther 2016 10 3;359(1):215-29. Epub 2016 Aug 3.

Departments of Bioengineering (H.C.L.), Pediatrics (A.G., Y.C., C.L., K.T.B., S.K.N.), Medicine (W.W., S.K.N.), Cellular and Molecular Medicine (S.K.N.), and Pharmacology (R.A.), and the San Diego Supercomputer Center (N.B., P.R.), University of California San Diego, La Jolla, California

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034704PMC
http://dx.doi.org/10.1124/jpet.116.232660DOI Listing
October 2016

Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein-Protein Encounters.

J Chem Theory Comput 2016 Jul 28;12(7):3236-49. Epub 2016 Jun 28.

Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center , C/Jordi Girona 29, Barcelona 08034, Spain.

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http://dx.doi.org/10.1021/acs.jctc.6b00204DOI Listing
July 2016

Adverse Effects of Cholinesterase Inhibitors in Dementia, According to the Pharmacovigilance Databases of the United-States and Canada.

PLoS One 2015 7;10(12):e0144337. Epub 2015 Dec 7.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144337PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671709PMC
June 2016

Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs.

Methods Mol Biol 2015 ;1335:295-311

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, MC 0684, 9500 Gilman Drive, San Diego, La Jolla, CA, 92093, USA.

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http://link.springer.com/10.1007/978-1-4939-2914-6_19
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http://dx.doi.org/10.1007/978-1-4939-2914-6_19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551442PMC
May 2016

X-ray structures of thioredoxin and thioredoxin reductase from Entamoeba histolytica and prevailing hypothesis of the mechanism of Auranofin action.

J Struct Biol 2016 May 12;194(2):180-90. Epub 2016 Feb 12.

Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jsb.2016.02.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003402PMC
May 2016

Towards a structural understanding of allosteric drugs at the human calcium-sensing receptor.

Cell Res 2016 05 22;26(5):574-92. Epub 2016 Mar 22.

Drug Discovery Biology, Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.

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http://dx.doi.org/10.1038/cr.2016.36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856764PMC
May 2016

An electrostatic mechanism for Ca(2+)-mediated regulation of gap junction channels.

Nat Commun 2016 Jan 12;7:8770. Epub 2016 Jan 12.

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

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http://dx.doi.org/10.1038/ncomms9770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730032PMC
January 2016

Shared Ligands Between Organic Anion Transporters (OAT1 and OAT6) and Odorant Receptors.

Drug Metab Dispos 2015 Dec 10;43(12):1855-63. Epub 2015 Sep 10.

Departments of Pediatrics (K.T.B., S.K.N.), Medicine (Division of Nephrology and Hypertension)(W.W., S.K.N.), Bioengineering (H.C.L.), Biomedical Sciences (C.Z.), School of Pharmacy/Pharmaceutical Science (R.A.), and Cellular and Molecular Medicine (S.K.N.), University of California, San Diego, La Jolla, California

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http://dx.doi.org/10.1124/dmd.115.065250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658493PMC
December 2015

High-quality and universal empirical atomic charges for chemoinformatics applications.

J Cheminform 2015 2;7:59. Epub 2015 Dec 2.

National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic.

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http://www.jcheminf.com/content/pdf/s13321-015-0107-1.pdf
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http://www.jcheminf.com/content/7/1/59
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http://dx.doi.org/10.1186/s13321-015-0107-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4667495PMC
December 2015

Molecular Mechanism of Action of Triazolobenzodiazepinone Agonists of the Type 1 Cholecystokinin Receptor. Possible Cooperativity across the Receptor Homodimeric Complex.

J Med Chem 2015 Dec 10;58(24):9562-77. Epub 2015 Dec 10.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States.

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http://dx.doi.org/10.1021/acs.jmedchem.5b01110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4790425PMC
December 2015

In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species.

Environ Sci Technol 2014 15;48(3):1964-72. Epub 2014 Jan 15.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.

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http://pubs.acs.org/doi/10.1021/es404568a
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http://dx.doi.org/10.1021/es404568aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951377PMC
October 2015

Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

Membranes (Basel) 2015 Oct 23;5(4):646-63. Epub 2015 Oct 23.

Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.

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http://dx.doi.org/10.3390/membranes5040646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704004PMC
October 2015

Molecular modeling and in vitro reactivation study between the oxime BI-6 and acetylcholinesterase inhibited by different nerve agents.

J Biomol Struct Dyn 2015 Sep 18;33(9):2048-58. Epub 2014 Dec 18.

a Laboratory of Molecular Modeling, Chemistry Department , Federal University of Lavras , Lavras , MG , Brazil.

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http://dx.doi.org/10.1080/07391102.2014.989408DOI Listing
September 2015

P16INK4a Upregulation Mediated by SIX6 Defines Retinal Ganglion Cell Pathogenesis in Glaucoma.

Mol Cell 2015 Sep 10;59(6):931-40. Epub 2015 Sep 10.

Shiley Eye Institute, Department of Ophthalmology and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Veterans Administration Healthcare System, San Diego, CA 92093, USA. Electronic address:

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http://www.cell.com/cms/attachment/2036665106/2051544793/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S109727651500585
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http://dx.doi.org/10.1016/j.molcel.2015.07.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648709PMC
September 2015

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.

Future Med Chem 2014 ;6(16):1741-55

Bioinformatics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.4155/fmc.14.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285145PMC
August 2015

Lanosterol reverses protein aggregation in cataracts.

Nature 2015 Jul 22;523(7562):607-11. Epub 2015 Jul 22.

1] Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China [2] State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China [3] Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California San Diego, La Jolla, California 92093, USA [4] Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, USA [5] Veterans Administration Healthcare System, San Diego, California 92093, USA.

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July 2015

Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity.

PLoS One 2014 13;9(5):e97514. Epub 2014 May 13.

Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019636PMC
June 2015

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

J Chem Inf Model 2015 Jun 11;55(6):1088-97. Epub 2015 Jun 11.

†National Centre for Biomolecular Research, Faculty of Science, and CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.

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http://pubs.acs.org/doi/10.1021/ci500758w
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http://dx.doi.org/10.1021/ci500758wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098400PMC
June 2015

Structure-based predictions of activity cliffs.

J Chem Inf Model 2015 May 11;55(5):1062-76. Epub 2015 May 11.

†Department of Drug Discovery and Development-Computation, IIT-Istituto Italiano di Tecnologia, 16163 Genova, Italy.

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http://dx.doi.org/10.1021/ci500742bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4553268PMC
May 2015

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

J Chem Theory Comput 2015 May 2;11(5):2167-2186. Epub 2015 Apr 2.

Molsoft L.L.C. , 11199 Sorrento Valley Road, S209, San Diego, California 92121, United States.

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http://dx.doi.org/10.1021/ct501138cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431507PMC
May 2015

Computational evidence for the reactivation process of human acetylcholinesterase inhibited by carbamates.

Comb Chem High Throughput Screen 2014 ;17(6):554-64

Chemistry Department, Federal University of Lavras, Campus Universitario, 3037, 37200-000, Lavras, MG, Brazil.

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http://dx.doi.org/10.2174/1386207316666131217100416DOI Listing
April 2015

Activation of Gαi at the Golgi by GIV/Girdin imposes finiteness in Arf1 signaling.

Dev Cell 2015 Apr 9;33(2):189-203. Epub 2015 Apr 9.

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2015.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4415880PMC
April 2015

Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine.

Science 2015 Mar 22;347(6226):1117-22. Epub 2015 Jan 22.

University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1126/science.1261064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362693PMC
March 2015

Histidine(7.36(305)) in the conserved peptide receptor activation domain of the gonadotropin releasing hormone receptor couples peptide binding and receptor activation.

Mol Cell Endocrinol 2015 Feb 9;402:95-106. Epub 2015 Jan 9.

Medical Research Council Receptor Biology Research Unit, Institute of Infectious Diseases and Molecular Medicine, Division of Medical Biochemistry, University of Cape Town Health Sciences Faculty, Observatory, Cape Town 7925, South Africa; School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Private bag 3, Wits 2050, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.mce.2015.01.008DOI Listing
February 2015

Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding.

Mol Pharmacol 2015 Jan 15;87(1):130-40. Epub 2014 Oct 15.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)

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http://dx.doi.org/10.1124/mol.114.095430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279081PMC
January 2015

A general method for site specific fluorescent labeling of recombinant chemokines.

PLoS One 2014 28;9(1):e81454. Epub 2014 Jan 28.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904831PMC
December 2014

Structure-based design, synthesis, and biological evaluation of isatin derivatives as potential glycosyltransferase inhibitors.

Chem Biol Drug Des 2014 Dec 14;84(6):685-96. Epub 2014 Aug 14.

Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.

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http://dx.doi.org/10.1111/cbdd.12361DOI Listing
December 2014

Discovery of novel membrane binding structures and functions.

Biochem Cell Biol 2014 Dec 18;92(6):555-63. Epub 2014 Sep 18.

a Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1139/bcb-2014-0074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267288PMC
December 2014

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 2;111(50):E5363-72. Epub 2014 Dec 2.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093

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http://dx.doi.org/10.1073/pnas.1417037111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4273337PMC
December 2014

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 13;141(1):188-97. Epub 2014 Jun 13.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093

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http://dx.doi.org/10.1093/toxsci/kfu114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271121PMC
September 2014

Sequence-conserved and antibody-accessible sites in the V1V2 domain of HIV-1 gp120 envelope protein.

AIDS Res Hum Retroviruses 2014 Sep 14;30(9):927-31. Epub 2014 Aug 14.

1 Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York.

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http://www.liebertpub.com/doi/10.1089/aid.2014.0034
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http://dx.doi.org/10.1089/AID.2014.0034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151074PMC
September 2014

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.

Structure 2014 Aug 24;22(8):1120-1139. Epub 2014 Jul 24.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92039, USA. Electronic address:

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http://dx.doi.org/10.1016/j.str.2014.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4126895PMC
August 2014

Compound activity prediction using models of binding pockets or ligand properties in 3D.

Curr Top Med Chem 2012 ;12(17):1869-82

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085113PMC
http://dx.doi.org/10.2174/156802612804547335DOI Listing
April 2014

PeptiSite: a structural database of peptide binding sites in 4D.

Biochem Biophys Res Commun 2014 Mar 6;445(4):717-23. Epub 2014 Jan 6.

UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2013.12.132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975830PMC
March 2014

Identification of novel serotonin transporter compounds by virtual screening.

J Chem Inf Model 2014 Mar 26;54(3):933-43. Epub 2014 Feb 26.

Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT, The Arctic University of Norway , 9037 Tromsø, Norway.

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http://dx.doi.org/10.1021/ci400742sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982395PMC
March 2014

The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers.

Mol Pharmacol 2014 Feb 11;85(2):301-9. Epub 2013 Nov 11.

Department of Pharmacology (D.P.K.), Department of Molecular Physiology and Biological Physics (S.A.L., M.P., H.F., M.C., R.F., M.Y.), Cardiovascular Research Center (M.A.M., R.F., M.Y.), Center for Membrane Biology (M.Y.), and Department of Medicine, Division of Cardiovascular Medicine (M.Y.), University of Virginia School of Medicine, Charlottesville, Virginia; the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (F.M.M., R.A.); and the La Jolla Institute for Allergy and Immunology (J.L.), La Jolla, California.

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http://dx.doi.org/10.1124/mol.113.088682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913357PMC
February 2014

Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors.

Mol Pharmacol 2013 Dec 10;84(6):794-807. Epub 2013 Sep 10.

Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California (P.C., W.L., V.C., R.C.S., V.K.); Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia (J.R.L., M.C.); and Skaggs School of Pharmacy and Pharmaceutical Sciences, and San Diego Supercomputer Center, University of California, San Diego, La Jolla, California (R.A.).

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http://dx.doi.org/10.1124/mol.113.088054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834142PMC
December 2013

BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

BMC Struct Biol 2013 Dec 13;13:32. Epub 2013 Dec 13.

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1186/1472-6807-13-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924234PMC
December 2013

Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5).

Theor Biol Med Model 2013 Sep 14;10:56. Epub 2013 Sep 14.

Medical Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø No-9037, Norway.

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http://dx.doi.org/10.1186/1742-4682-10-56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848485PMC
September 2013

Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening.

J Chem Inf Model 2013 Aug 25;53(8):2131-40. Epub 2013 Jul 25.

Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China.

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http://dx.doi.org/10.1021/ci400203fDOI Listing
August 2013

Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases.

Annu Rev Pharmacol Toxicol 2013 22;53:331-54. Epub 2012 Oct 22.

Department of Oncology and Diagnostic Sciences, Department of Pathology, and Greenebaum Cancer Center, University of Maryland, Baltimore, Maryland 21201, USA.

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http://dx.doi.org/10.1146/annurev-pharmtox-010510-100608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4074518PMC
July 2013

Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor.

J Biol Chem 2013 Jul 10;288(29):21082-95. Epub 2013 Jun 10.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona 85259, USA.

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http://dx.doi.org/10.1074/jbc.M113.480715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774375PMC
July 2013

Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics.

Int J Quantum Chem 2013 Jun;113(12):1669-1675

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA, 92093.

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http://dx.doi.org/10.1002/qua.24400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235788PMC
June 2013

Viral infection controlled by a calcium-dependent lipid-binding module in ALIX.

Dev Cell 2013 May 9;25(4):364-73. Epub 2013 May 9.

Biochemistry Department, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva 4, Switzerland.

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https://linkinghub.elsevier.com/retrieve/pii/S15345807130019
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http://dx.doi.org/10.1016/j.devcel.2013.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129370PMC
May 2013

Predicting p Ka values from EEM atomic charges.

J Cheminform 2013 Apr 10;5(1):18. Epub 2013 Apr 10.

National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.

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http://dx.doi.org/10.1186/1758-2946-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663834PMC
April 2013

The GPCR Network: a large-scale collaboration to determine human GPCR structure and function.

Nat Rev Drug Discov 2013 01 14;12(1):25-34. Epub 2012 Dec 14.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

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http://www.nature.com/articles/nrd3859
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http://dx.doi.org/10.1038/nrd3859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723354PMC
January 2013