Amy Y. Shih

Current Location:
Johnson & Johnson PRD, LLC.
3210 Merryfield Row
San Diego, CA 92121

Education

Research

lipoproteins
  • Assembly and maturation of nanodiscs and lipoproteins
  • Coarse-grained molecular dynamics
  • Structure and function of cytochrome P450s
  • Conformational changes in MAP Kinases

For information about my previous research on antimicrobial nanoemulsions goto M-NiMBS and NanoBio

Publications

Publications Database

Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance. Aleksandra Kijac, Amy Y. Shih, Andrew J. Nieuwkoop, Klaus Schulten, Stephen G. Sligar, and Chad Rienstra. Biochemistry, 49:9190-9198, 2010.

Maturation of high-density lipoproteins. Amy Y. Shih, Stephen G. Sligar, and Klaus Schulten. Journal of the Royal Society Interface, 6:863-871, 2009.

Molecular models need to be tested: the case of a solar flares discoidal HDL model. Amy Y. Shih, Stephen G. Sligar, and Klaus Schulten. Biophysical Journal, 94:L87-L89, 2008.

Assembly of lipids and proteins into lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Journal of Physical Chemistry B, 111:11095-11104, 2007.

Disassembly of nanodiscs with cholate. Amy Y. Shih, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten. Nano Letters, 7:1692-1696, 2007.

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Journal of Structural Biology, 157:579-592, 2007.

Coarse grained protein-lipid model with application to lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry B, 110:3674-3684, 2006.

The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.

Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, and Klaus Schulten. Biophysical Journal, 88:548-556, 2005.

A rapid staining technique for the detection of the initiation of germination of bacterial spores. Tarek Hamouda, Amy Y. Shih, and James R. Baker Jr. Letters in Applied Microbiology, 34:86-90, 2002

A novel surfactant nanoemulsion with a unique non-irritant topical antimicrobial activity against bacteria, enveloped viruses and fungi. Tarek Hamouda, Andrzej Myc, Brian Donovan, Amy Y. Shih, Jon D. Reuter, and James R. Baker Jr. Microbiological Research, 156:1-7, 2001.

Book Chapters

Publications Database

Molecular modeling of the structural properties and formation of high-density lipoprotein particles. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, Stephen G. Sligar, and Klaus Schulten. In Scott Feller, editor, Current Topics in Membranes: Computational Modeling of Membrane Bilayers, chapter 11, pp. 313-342. Elsevier, 2008.

Application of residue-based and shape-based coarse graining to biomolecular simulations. Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.

Computer modeling in biotechnology, a partner in development. Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.

Presentations

Maturation of high-density lipoprotein particles. A.Y. Shih. Telluride Science Research Center workshop on mechanistic analysis of biological systems with novel computational models, 2008, Telluride, CO

The maturtion of human high-density lipoprotein particles: conversion from disks to spheres. A.Y. Shih, S.G. Sligar, and K. Schulten. Biophysical Society Meeting, 2008. Long Beach, CA

Assembly of lipoproteins revealed by coarse-grained molecular dynamics simulations. A.Y. Shih, P.L. Freddolino, A. Arkhipov, S.G. Sligar, and K. Schulten. Biophysical Society Meeting, 2007. Baltimore, MD

Disassembly of nanodiscs: using coarse-grained MD for insight into self-assembly. A.Y. Shih, P.L. Freddolino, S.G. Sligar, and K. Schulten. Biophysical Society Meeting, 2007. Baltimore, MD

A coarse grained protein-lipid model with application to high-density lipoprotein particles. A.Y. Shih, A. Arkhipov, P.L. Freddolino, and K. Schulten. Biophysical Society Meeting, 2006. Salt Lake City, UT

Molecular dyanmics simulations of discoidal bilayers assembled from truncated human lipoproteins. A.Y. Shih, I.G. Denisov, J.C. Phillips, S.G. Sligar and K. Schulten. Biophysical Society Meeting, 2005. Long Beach, CA

Solution X-ray scattering from nanoscale phospholipid bilayer - protein systems. A.Y. Shih, T.H. Bayburt, I.G. Denisov, Y.V. Grinkova, M.A. Mclean, and S.G. Sligar. Advanced Photon Source Users Meeting, 2004. Argonne, IL

Decontaminatin of B. anthracis simulant from typical office environment surfaces using a novel nanoemulsion. A.Y. Shih, T. Hamouda, and J.R. Baker Jr. American Society for Microbiology General Meeting, 2001. Orlando, FL

Antimicrobial nanoemulsions useful for decontamination of food processing plants. E.L. Detweiler, A.Y. Shih, T. Hamouda, and J.R. Baker Jr. American Society for Microbiology General Meeting, 2001. Orlando, FL

Optimization of nanoemulsion sporicidal activity. T. Hamouda, A.Y. Shih, G. Morris, R. Tonda, and J.R. Baker Jr. American Society for Microbiology General Meeting, 2000. Los Angeles, CA

Environmental decontamination of B. globigii spores. A.Y. Shih, T. Hamouda, S. Saqqa, and J.R. Baker Jr. American Society for Microbiology General Meeting, 2000. Los Angeles, CA

Enhancing the bactericidal activity of surfactant lipid preparation. R. Tonda, G. Morris, A.Y. Shih, T. Hamouda, and J.R. Baker Jr. American Society for Microbiology General Meeting, 1999. Chicago, IL

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