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  • Welcome to the Amaro Lab
    chemistry biology physics and pharmacology our research integrates both applied and basic science components with goals to bridge the interface between basic and clinical research Fundamental enzymological and drug discovery studies are tightly coupled to a wide range of biochemical and biophysical experiments that allow us to engage in dynamic and exciting collaborations with various experimental labs Our work is sponsored by grants from the Regents of the University of

    Original URL path: https://amarolab.ucsd.edu/ (2015-07-15)
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  • Welcome to the Amaro Lab
    chemistry biology physics and pharmacology our research integrates both applied and basic science components with goals to bridge the interface between basic and clinical research Fundamental enzymological and drug discovery studies are tightly coupled to a wide range of biochemical and biophysical experiments that allow us to engage in dynamic and exciting collaborations with various experimental labs Our work is sponsored by grants from the Regents of the University of

    Original URL path: https://amarolab.ucsd.edu/Welcome.html (2015-07-15)
    Open archived version from archive

  • About the Amaro Lab
    make unprecedented contributions to drug discovery efforts Large scale simulations of increasingly realistic biological systems will allow us to investigate protein function and molecular recognition in atomic detail These investigations will help drive discovery efforts and experimental work on these systems in collaboration with leading experimentalists Our current investigations concern the neglected tropical diseases borne by the trypanosome organisms potentially pandemic avian influenza cancer Chlamydia and the cytochrome P450s Addressing Complexity in Molecular Recognition The current model for computer aided drug design is simply to take one or a few crystallographic structure s of a protein receptor and design a single molecule to block its activity Though this model has had some success more sophisticated drug discovery and design methodologies will significantly increase the chances of scientists being able to design more effective drugs faster Our work in this area focuses primarily on three major goals the incorporation of receptor flexibility investigating mechanisms of drug and antiviral resistance and disease network pharmacology Multiscale control mechanisms in nitrogen metabolism Central to understanding the complex inner workings of the cell will be expanding our knowledge of the cellular machinery driving the vast assembly of processes that sustain life The major workhorses of

    Original URL path: https://amarolab.ucsd.edu/about.html (2015-07-15)
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  • Members of the Amaro Lab
    Postila Graduate Students Tavina Claiborne Sasha Heyneman Sophia Hirakis Christopher Lee Pek leong Aline Oliveira Visiting Jamie Schiffer Lane Votapka Jeffrey Wagner Undergraduates Others Garrett Chan Kevin Cheng Nathan Hensley Chriag Krishna Timothy Lin Celia Wong High School Students Divya Ghoshal Ezra Kosviner Michael Murphy Taylor Perison Clare Zhu Alumni Brian Atwood Meghan Cain Eric Chen Harvard Rob Langer Lab Luke Czapla Adam Gonzales Sharon Grubner Rachel Li Wilfred Li

    Original URL path: https://amarolab.ucsd.edu/members.html (2015-07-15)
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  • News from the Amaro Lab
    a helix capping residue by constraining the mobility of loop 7 and helping to create a novel binding pocket that favorably accommodates cytosine August 2 2013 Sophia was awarded a research fellowship from the Interfaces Graduate Training Program at UCSD This PhD specialization in Multi scale Biology will augment her graduate research in Chemistry with interdisciplinary training she will use Molecular Brownian Dynamics to investigate the molecular behavior of the Ryanodine Receptor RyR in the hippocampus Biophysical simulations imaging studies with NCMIR the Ellisman lab cellular simulations using MCell with the Sejnowski lab will be integrated for a more holistic study of RyR July 15 2013 The beta version of the Amaro Lab website has been launched Explore and enjoy July 2013 Congratulations to Jason and Luke for their recently accepted paper in the Journal of Chemical Information and Modeling Jason and Luke have presented a new molecular understanding of ligand recognition in the cytochrome P450 enzyme aromatase which is a major target for breast cancer therapeutics July 2013 Congratulations to Vicki for her recent article in PLOS One Vicki played a heroic role in determining a homology model for the core barrel structure of the leading vaccine target in

    Original URL path: https://amarolab.ucsd.edu/news.html (2015-07-15)
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  • Publications from the Amaro Lab
    QSPR Chemical Biology and Drug Discovery Special Issue Beyond the 100 Dollar Genome 81 61 71 2013 RETURN TO TOP Yr 2012 38 Swift R V Ong C D Amaro R E Magnesium Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme Biochemistry 51 51 10236 43 doi 10 1021 bi301224b 2012 37 Nichols S E Swift R V and Amaro R E Structure Based Prediction with Molecular Dynamics for Hit Identification Current Topics in Medicinal Chemistry 12 18 2002 2012 2012 36 Votapka L Amaro R E Multistructural Hot Spot Characterization with FTProd BMC Bioinformatics doi 10 1093 bioinformatics bts689 2012 35 Jansen J M Amaro R E Cornell W Tseng Y J Walters W P Computational Chemistry and Drug Discovery A call to action Future Medicinal Chemistry 4 1893 1896 2012 34 Jansen J M Cornell W Tseng Y J Amaro R E Teach Discover Treat TDT Collaborative Drug Discovery for Neglected Diseases Journal of Molecular Graphics and Modelling 38 360 362 2012 33 VanWart A T Eargle J Schulten Z Amaro R E Exploring Residue Component Contributions to Dynamical Network Models of Allostery Journal of Computational and Theoretical Chemistry dx doi org 10 1021 ct300377a 2012 32 Votapka L Demir Ö Swift R V Walker R C Amaro R E Variable ligand and receptor binding hot spots in key strains of influenza neuraminidase Journal of Molecular Genetics and Medicine 6 293 300 2012 31 Demir O Amaro R E Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2 J Chem Inf Model doi 10 1021 ci3001327 2012 30 Gabrielsen M Beckham K S H Feher V A Zetterström C E Wang D Muller S Elofsson M Amaro R E Byron O Roe A Structural Characterisation of Tpx from Yersinia pseudotuberculosis Reveals Insights into the Binding of Salicylidene Acylhydrazide Compounds PLoS ONE 7 2 e32217 doi 10 1371 journal pone 0032217 2012 29 Votapka L W Czapla L Zhenirovskyy M Amaro R E DelEnsembleElec Computing ensemble averaged electrostatics using DelPhi Communications in Chemical Physics 13 256 268 doi 10 4208 cicp 170711 111111s 2012 RETURN TO TOP Yr 2011 28 Swift R V and Amaro R E Modeling the Pharmacodynamics of Passive Membrane Permeability Journal of Computer Aided Molecular Design 1007 1017 doi 10 1007 s10822 011 9480 7 2011 27 Torres R Swift R V Chim N Wheatley N Lan B Atwood B R Pujol C Sankaran B Bliska J B Amaro R E and Goulding C Biochemical Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis PLoS One 6 9 e25084 doi 10 1371 journal pone 0025084 2011 26 Demir O Baronio R Salehi F Wassman C Hall L Hatfield G Wesley Chamberlin A R Kaiser P Lathrop R H Amaro R E Ensemble based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants PLoS Computational Biology 7 10 e1002238 doi 10 1371 journal pcbi 1002238 2011 25 Amaro R E Swift R V Votapka

    Original URL path: https://amarolab.ucsd.edu/publications.html (2015-07-15)
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  • Highlights of the Amaro Lab
    the vast potential each Learn More New Target for Treating Wide Range of Cancers The finding heralds a new treatment approach as mutant forms of this protein are implicated Learn More ISU College of Pharmacy Hosts Lecturer Dr Rommie Amaro ISU Idaho State University College of Pharmacy recently hosted Dr Rommie Amaro as the Learn More UC San Diego Researchers Identify Potential New Drug Candidates Using protein structures generated by

    Original URL path: https://amarolab.ucsd.edu/highlights.html (2015-07-15)
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  • Resources from the Amaro Lab
    and execution system The tool assists users in the set up and execution of publication quality MD research including multi stage minimization heating constrained equilibration and multi copy production dynamics The tool runs on local GPU s and GPU clusters and the tutorial introduces users to both platforms CEBA Dataset Developed by Jesper Sørensen A dataset for Possion Boltzmann calculations on biomolecule ligand systems This is a subset of the data presented in the book Computational Electrostatics for Biological Applications Eds W Rocchia M Spagnuolo The dataset contains structure files in various required formats input files for PBSA APBS and DelPhi DelEnsembleElec Developed by Lane Votapka and Luke Czapla A plugin for VMD that interfaces with the electrostatics solver DelPhi to provide single frame or ensemble averaged electrostatic calculations using the Poisson Boltzmann equation Allows extensive customization of Delphi input parameters and many other features FTProd Developed by Lane Votapka To merely consider a single frozen structure of a protein important information may be neglected Proteins constantly move change shape and mutate FTProd allows a researcher to consider this fluctuations in the analysis and prediction of ligand binding hot spots WISP Developed by Jacob Durrant Lane Votapka and Adam Van

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