__________________________________________________________________________ Elaine C. Meng, PhD Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco, CA 94143-2240 meng@cgl.ucsf.edu http://www.rbvi.ucsf.edu/home/meng/index.html __________________________________________________________________________ SUMMARY I'm a writer/editor with expertise in chemistry, structural biology, molecular modeling, and the biomedical sciences. I have a pharmacy degree, experience in computational chemistry, and a commitment to continuing education driven by curiosity and interest. In my projects, I strive to combine an artistic sensibility with clarity, accuracy, and attention to detail. Currently, I test, document, and help to design features of the molecular modeling program UCSF Chimera and its successor, ChimeraX. I also create tutorials and related online content, including molecular graphics images and animations, and answer questions from users worldwide. I participate in writing grant applications, reports to funding agencies, and manuscripts for publication. I'm the primary author of over a dozen peer-reviewed publications, and a coauthor of many more. EDUCATION Graduate School (1988-1993) Department of Pharmaceutical Chemistry University of California, San Francisco, California Advisor: Irwin D. Kuntz Thesis: Tools for Ligand Discovery and Design: Molecular Docking and Structural Databases Ph.D. Pharmaceutical Chemistry, March 1993 College (1983-1988) Andrews University, Berrien Springs, Michigan (1983-1984) Wright State University, Dayton, Ohio (1984-1985) University of Cincinnati College of Pharmacy, Cincinnati, Ohio (1985-1988) B.S. Pharmacy, June 1988 PROFESSIONAL EXPERIENCE University of California, San Francisco (UCSF) Jul 2006-present Specialist 1996-Jun 2006 Assistant Researcher 1996-1997,1999-present Resource for Biocomputing, Visualization, and Informatics (Thomas Ferrin, P.I.; Dept. of Pharmaceutical Chemistry) Feb 2002-May 2017 Laboratory of Patricia Babbitt (Biopharmaceutical Sciences, Pharmaceutical Chemistry) 1998-Jan 2002 Laboratory of Henry Bourne (Cellular and Molecular Pharmacology) 1998-2000 Laboratory of Fred Cohen (Cellular and Molecular Pharmacology) 1996-1997 Laboratory of Peter Kollman (Pharmaceutical Chemistry) 1993-1995 Postdoc: solvation free energies, polarizable potentials Mentor: Peter A. Kollman 1988-1993 Graduate Student: molecular docking, structural databases Mentor: Irwin D. Kuntz 1988-1989 Teaching Assistant: medicinal chemistry series Merrell Dow Research Institute, Cincinnati, Ohio 1987-1988 Research Assistant: pharmacophore mapping University of Cincinnati College of Pharmacy (UCCP) 1987-1988 Pharmacy Extern (Kettering Memorial Hospital, Kettering, OH; Miami Valley Hospital, Dayton, OH; Fidelity Prescriptions, Dayton, OH) 1986-1987 Pharmacy Intern (Gray Drugfair, Inc., Dayton, OH) 1986-1987 Tutor: Physical Pharmacy, Pharmaceutical Analysis & Control, Pharmacy Calculations OTHER TRAINING Entry Level Clinical Research Associate Training Course, held by the Drug Information Association at Marriott Fisherman's Wharf, San Francisco, September 1996 TECHNICAL SKILLS * writing for different audiences (scientists vs. general public) * adaptable stringency of editing (time constraints, client needs) * molecular graphics and modeling; Chimera/ChimeraX figures and movies * working in a team environment with version control (svn, git) * MS Word, EndNote, Google Docs * HTML, CSS * Unix, Mac * Fortran77 PUBLICATIONS (48) UCSF ChimeraX: Tools for structure building and analysis. Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE. Protein Sci. 2023 Nov;32(11):e4792. doi: 10.1002/pro.4792. PMID: 37774136 (47) The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE. Bioinformatics. 2023 Feb 3;39(2):btad080. doi: 10.1093/bioinformatics/btad080. PMID: 36759942 (46) scNetViz: From Single Cells to Networks Using Cytoscape. Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH. F1000Res. 2021 Jun 7;10:ISCB Comm J-448. doi: 10.12688/f1000research.52460.1. PMID: 34912541 (45) UCSF ChimeraX: Structure Visualization for Researchers, Educators, and Developers. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci. 2021 Jan;30(1):70-82. doi: 10.1002/pro.3943. PMID: 32881101 (44) Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH. F1000Res. 2019;8:296. doi: 10.12688/f1000research.18490.3. (https://doi.org/10.12688/f1000research.18490.3) (43) Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Methods Enzymol. 2018;606:1-71. doi: 10.1016/bs.mie.2018.06.004. PMID: 30097089 (42) Molecular Visualization on the Holodeck. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. J Mol Biol. 2018 Oct 19;430(21):3982-3996. doi: 10.1016/j.jmb.2018.06.040. PMID: 29964044 (41) UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis. Goddard TG, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. Protein Sci. 2018 Jan;27(1):14-25. PMID: 28710774 (40) Biocuration in the Structure-Function Linkage Database: The Anatomy of a Superfamily. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Database (Oxford). 2017 Jan 1;2017(1). PMID: 28365730 (39) Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W478-84. PMID: 24861624 (38) The Structure-Function Linkage Database. Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. PMID: 24271399 (37) UCSF Chimera, MODELLER, and IMP: an integrated modeling system. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. J Struct Biol. 2012 Sep;179(3):269-78. PMID: 21963794 (36) Topological variation in the evolution of new reactions in functionally diverse enzyme superfamilies. Meng EC, Babbitt PC. Curr Opin Struct Biol. 2011 Jun;21(3):391-7. PMID: 21458983 (35) ModBase, a database of annotated comparative protein structure models, and associated resources. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. Nucleic Acids Res. 2011 Jan;39(Database issue):D465-74. PMID: 21097780 (34) Computational tools for the interactive exploration of proteomic and structural data. Morris JH, Meng EC, Ferrin TE. Mol Cell Proteomics. 2010 Aug;9(8):1703-15. PMID: 20525940 (33) DOCK 6: combining techniques to model RNA-small molecule complexes. Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo RC, Case DA, James TL, Kuntz ID. RNA. 2009 Jun;15(6):1219-30. PMID: 19369428 (32) 3D motifs. Meng EC, Polacco BJ, Babbitt PC. In: From Protein Structure to Function with Bioinformatics. Rigden, DJ, editor. Springer 2009, XVI, 187-216. Nilmeier JP, Meng EC, Polacco BJ, Babbitt PC. 2nd edition, Springer 2017, 361-392. (31) Evolution of function in the "two dinucleotide binding domains" flavoproteins. Ojha S, Meng EC, Babbitt PC. PLoS Comput Biol. 2007 Jul;3(7):e121. PMID: 17658942 (30) Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics. 2006 Jul 12;7:339. PMID: 16836757 (29) Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Biochemistry. 2006 Feb 28;45(8):2545-55. PMID: 16489747 (28) The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D642-8. PMID: 16381950 (27) Apolipoprotein (apo) E4 enhances amyloid beta peptide production in cultured neuronal cells: apoE structure as a potential therapeutic target. Ye S, Huang Y, Müllendorff K, Dong L, Giedt G, Meng EC, Cohen FE, Kuntz ID, Weisgraber KH, Mahley RW. Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18700-5. PMID: 16344478 (26) UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12. PMID: 15264254 (25) Superfamily active site templates. Meng EC, Polacco BJ, Babbitt PC. Proteins. 2004 Jun 1;55(4):962-76. PMID: 15146493 (24) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O. J Biol Chem. 2004 Feb 27;279(9):8126-32. PMID: 14660595 (23) The Structure Superposition Database. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. Nucleic Acids Res. 2003 Jan 1;31(1):505-10. PMID: 12520064 (22) BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE. Nucleic Acids Res. 2003 Jan 1;31(1):278-81. PMID: 12520002 (21) Constitutive activation and endocytosis of the complement factor 5a receptor: evidence for multiple activated conformations of a G protein-coupled receptor. Whistler JL, Gerber BO, Meng EC, Baranski TJ, von Zastrow M, Bourne HR. Traffic. 2002 Dec;3(12):866-77. PMID: 12453150 (20) Receptor activation: what does the rhodopsin structure tell us? Meng EC, Bourne HR. Trends Pharmacol Sci. 2001 Nov;22(11):587-93. Review. PMID: 11698103 (19) Mutant G protein alpha subunit activated by Gbeta gamma: a model for receptor activation? Rondard P, Iiri T, Srinivasan S, Meng E, Fujita T, Bourne HR. Proc Natl Acad Sci U S A. 2001 May 22;98(11):6150-5. PMID: 11344266 (18) An activation switch in the ligand binding pocket of the C5a receptor. Gerber BO, Meng EC, Dotsch V, Baranski TJ, Bourne HR. J Biol Chem. 2001 Feb 2;276(5):3394-400. PMID: 11062244 (17) Rhodopsin sees the light. Bourne HR, Meng EC. Science. 2000 Aug 4;289(5480):733-4. PMID: 10950717 (16) Evaluating non-bonded parameters for zinc in DOCK. Vaz RJ, Kuntz ID, Meng EC. Med Chem Res. 1999;9(7-8):479-89. (15) Similar structures and shared switch mechanisms of the beta2-adrenoceptor and the parathyroid hormone receptor. Zn(II) bridges between helices III and VI block activation. Sheikh SP, Vilardarga JP, Baranski TJ, Lichtarge O, Iiri T, Meng EC, Nissenson RA, Bourne HR. J Biol Chem. 1999 Jun 11;274(24):17033-41. PMID: 10358054 (14) C5a receptor activation. Genetic identification of critical residues in four transmembrane helices. Baranski TJ, Herzmark P, Lichtarge O, Gerber BO, Trueheart J, Meng EC, Iiri T, Sheikh SP, Bourne HR. J Biol Chem. 1999 May 28;274(22):15757-65. PMID: 10336477 (13) Molecular dynamics studies of the properties of water around simple organic solutes. Meng EC, Kollman PA. J Phys Chem. 1996;100:11460-70. (12) Investigating the anomalous solvation free energies of amines with a polarizable potential. Meng EC, Caldwell JW, Kollman PA. J Phys Chem. 1996;100:2367-71. (11) Challenges in structure-based drug design. Kuntz ID, Meng EC, Shoichet BK. In: New Perspectives in Drug Design. Academic Press Ltd. 1995, 137-153. (10) Accurate solvation free energies of acetate and methylammonium ions calculated with a polarizable water model. Meng EC, Cieplak P, Caldwell JW, Kollman PA. J Am Chem Soc. 1994;116:12061-2. (9) Molecular docking: A tool for ligand discovery and design. Meng EC, Kuntz ID. (1994) Drug Inf J. 1994;28:735-49. (8) Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. Meng EC, Kuntz ID, Abraham DJ, Kellogg GE. J Comput Aided Mol Des. 1994 Jun;8(3):299-306. PMID: 7964929 (7) A discussion of various computational methods for drug design. Lewis RA, Meng EC. In: Molecular Modelling and Drug Design. Vinter JG, Gardner M, editors. Macmillan, London 1994, 170-210. (6) Receptor-based molecular design. Kuntz ID, Meng EC, Shoichet BK. Acc Chem Res. 1994;27:117-23. (5) Orientational sampling and rigid-body minimization in molecular docking. Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Proteins. 1993 Nov;17(3):266-78. PMID: 8272425 (4) Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. Rutenber E, Fauman EB, Keenan RJ, Fong S, Furth PS, Ortiz de Montellano PR, Meng E, Kuntz ID, DeCamp DL, Salto R, Rose JR, Crak CS, Stroud RM. J Biol Chem. 1993 Jul 25;268(21):15343-6. PMID: 8340363 (3) Automated docking with grid-based energy evaluation. Meng EC, Shoichet BK, Kuntz ID. J Comput Chem. 1992;13:505-24. (2) Determination of molecular topology and atomic hybridization states from heavy atom coordinates. Meng EC, Lewis RA. J Comput Chem. 1991;12:891-8. (1) A novel synthesis of xanthines: support for a new binding mode for xanthines with respect to adenosine at adenosine receptors. Peet NP, Lentz NL, Meng EC, Dudley MW, Ogden AM, Demeter DA, Weintraub HJ, Bey P. J Med Chem. 1990 Dec;33(12):3127-30. PMID: 2258897 HONORS/ AWARDS 1993 Drug Information Association Dissertation Summary Award 1992-1993 Chancellor's Fellowship (UCSF) 1991-1992 NIH Traineeship (UCSF) 1989-1991 Graduate Opportunity Fellowship (UCSF) 1989 Joseph M. Long Foundation Award for Excellence in Teaching (UCSF) 1988-1989 Regents Fellowship (UCSF) 1988 Rho Chi Academic Achievement Award (UCCP) 1988 Proctor & Gamble Research and Scholarly Activity Award (UCCP) 1987-1988 Rho Chi Pharmacy Honor Society (UCCP) 1987 Merck, Sharp, & Dohme Award (UCCP) 1986 American Institute of the History of Pharmacy Award (UCCP) 1985-1988 James E. Koffenberger Scholarship (UCCP) 1984 CRC Press Freshman Chemistry Award (Andrews U.) 1983 National Merit Scholarship (Andrews U.) 1983 Valedictory (Spring Valley Academy) 1981-1983 National Honor Society (Spring Valley Academy, Centerville, OH) 1981 National Guild of Piano Teachers Paderewski Medal PROFESSIONAL ASSOCIATIONS American Pharmacists Association __________________________________________________________________________