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  • Welcome to the Amaro Lab
    the latest innovations in theoretical chemistry to the experimental physical and biological sciences National Biomedical Computation Resource NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes Teaching CHEM 167 Medicinal Chemistry 2013 CHEM 167 Syllabus CHEM 185 285 Computational Chemistry 2012 CHEM

    Original URL path: https://amarolab.ucsd.edu/contactus.html (2015-07-15)
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  • Principal Investigator: Dr. Rommie Amaro
    Professor Zan Luthey Schulten where she worked mainly on computational methods to reconstruct free energy profiles from non equilibrium pulling experiments of ammonia conduction through a beta barrel protein involved in histidine biosynthesis and studying mechanisms of allosteric regulation in proteins While a graduate student she also worked closely with the National Institutes of Health NIH Resource for Macromolecular Modeling and Bioinformatics led by Professor Klaus Schulten where she helped develop a series of workshops that have now been taught worldwide After earning her Ph D Dr Amaro went on to receive a NIH Kirschstein National Research Service Award NRSA postdoctoral fellowship and worked under the tuteledge of the Howard Hughes Medical Investigator and National Academy of Sciences member Professor J Andrew McCammon at University of California San Diego UCSD In 2009 Dr Amaro started her independent research career in the Deparments of Pharmaceutical Sciences Computer Science and Chemistry at the University of California Irvine In 2010 she was selected as an NIH New Innovator for her work developing cutting edge computational methods to help discover new drugs The following year she received the Presidential Early Career Award for Scientists and Engineers In 2012 Dr Amaro opened her lab at

    Original URL path: https://amarolab.ucsd.edu/people_pi.html (2015-07-15)
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  • Current Members of the Amaro Lab
    of Biological Sciences Before coming to graduate school Sophie attended Manhattan College in Riverdale NY There she worked in the organic chemistry research lab of Dr James McCullagh She received her Bachelors of Science degree in Biochemistry in 2011 Her primary research interests include brownian dynamics simulations and sub cellular modeling of calcium dynamics in cardiac myocytes Her favorite protein is the ryanodine receptor 2 RyR2 Sophie s hobbies involve singing dancing and listening to New York Yankees games on her radio Christopher Lee Influenza membrane glycoproteins hemagglutinin HA and neuraminidase NA are thought to mediate viral recognition attachment endocytosis and eventual release There is frequent mention in literature that the HA and NA binding affinities must be balanced for optimal viral function The rational for this hypothesis is that while HA must bind to host cell surface glycan receptors to promote cell entry it must not bind so tightly that emerging viral progeny are unable to exit the cell via the enzymatic action of NA My goal is to use multi scale computational models of viral surfaces to simulate key events in the host switching process Pek Ieong Pek Ieong is a newly graduated alumnus of UCSD with a Bachelor s degree in Pharmacological Chemistry She has resigned herself to the fact that because Ieong is such an unusual last name most of the time people will assume her surname to be Leong when they first see it Pek enjoys sleeping so much that her biggest dream in life is to hibernate in wintertime When she is not daydreaming about hibernation she can be found working in the lab or in class Aline Oliveira Aline is a visiting graduate student at UCSD in the Amaro Lab She has graduated with a degree in Chemistry from the Federal University of Lavras UFLA 2009 and received her Master Degree in Chemistry from the Military Institute of Engineering IME 2012 Brazil Currently she is a PhD student in Chemistry at the Chemistry Institute of São Carlos University of São Paulo IQSC USP Brazil She works with computational methods applied to medicinal chemistry such as QSAR molecular modeling docking and dynamics simulations Her PhD research aims to understand the main features related to the interactions between some antagonists and the sigma 1 receptor thus contributing for the rational drug design of new molecules for neuropathic pain treatment Her hobbies include traveling reading and spending time with her friends Jamie Schiffer Jamie received a B S in biochemistry and a minor in mathematics and biology from Boston University in the spring of 2012 While at Boston University Jamie played Division I soccer and pursued scientific research She worked in the synthetic organic laboratory of John Porco for a brief period before realizing her love for neurobiology and moved to the laboratory of Xue Han where she studied optogenetics She plans to pursue a joint Ph D as an experimental and computational biophysicist in the Amaro and Komives laboratories at UCSD Jamie s hobbies include

    Original URL path: https://amarolab.ucsd.edu/people_current.html (2015-07-15)
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  • AMBER GPU Molecular Dynamics (MD) Workflow Tool and Tutorial
    AMBER GPU Molecular Dynamics MD Workflow Tool and Tutorial Downloads MDWorkflow Tutorial Local GPU MDWorkflow Tutorial GPU Cluster Input Files zip MD WF SingleSys zip Amaro Lab Home

    Original URL path: https://amarolab.ucsd.edu/mdworkflow/mdworkflow.html (2015-07-15)
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  • DelEnsembleElec
    CEBA Dataset Subset of dataset used in Biomolecule Ligand Poisson Boltzman Calculations in Computational Electrostatics for Biological Applications Eds W Rocchia M Spagnuolo Download dataset Content description Amaro Lab Home

    Original URL path: https://amarolab.ucsd.edu/CEBA_Dataset.html (2015-07-15)
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  • DelEnsembleElec
    Allows extensive customization of Delphi input parameters and many other features Requires DelPhi to operate Download DelPhi here Tutorial Learn how to use DelEnsembleElec with a simple tutorial DelEnsembleElec is freely available under the GNU public license If you have

    Original URL path: https://amarolab.ucsd.edu/delensembleelec.html (2015-07-15)
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  • FTProd - Main Page
    It also requres output from the program FTMAP Download VMD FTMAP server Amaro Lab Home Getting Started Download This package includes relevant FTProd scripts and programs as well as installation instructions Tutorial Learn how to use FTProd with this short step by step tutorial Proteins are dynamic entities To merely consider a single frozen structure of a protein important information may be neglected Proteins constantly move change shape and mutate

    Original URL path: https://amarolab.ucsd.edu/ftprod/ (2015-07-15)
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  • DelEnsembleElec Tutorial: Home
    Chemistry and Biochemistry University of California San Diego Using DelEnsembleElec An Electrostatics Plugin for VMD Plugin Developer Lane Votapka Contributors Rommie Amaro Luke Czapla Maxim Zhenirovskyy Contents Installation Single Frame Electrostatics Ensemble Averaged Electrostatics Troubleshooting Download Tutorial Files Back to

    Original URL path: https://amarolab.ucsd.edu/delphielectut/de_home.html (2015-07-15)
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