VirusSlidesFinal

Slide1: 

VirusX Quantitative Multi-Scale Virus Simulation for Bio-Threat Reduction Center for Cell and Virus Theory Indiana University Bloomington IN 47405 Director: P. Ortoleva ortoleva@indiana.edu (812)855-2717 Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

VirusX Applications: 

VirusX Applications Drug and vaccine design Predict properties of automatically generated strains of known viruses Design disinfection and containment strategies Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

VirusX Whole Virus Modeling: 

VirusX Whole Virus Modeling Input to Output Relations Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Abundant Viral Structural Data Exists: 

Abundant Viral Structural Data Exists There are 2074 structures of viruses available of more than 5,450 known viruses belonging to over 2000 species, 287 genera, 73 families and 3 orders. http://www-micro.msb.le.ac.uk/3035/VirusGroups.html http://mmtsb.scripps.edu/viper htpp://www.pdb.org Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Quantified Predictions With VirusX: 

Quantified Predictions With VirusX Methods are needed to compute how viral structure and stability change in biofluids and intra-cellular medium. CHARMM and AMBER calibrated force fields Poisson-Boltzmann charge and dielectric properties database X-ray determined protein and whole-virus structure as initial configurations Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

VirusX Whole Virus Modeling: 

VirusX Whole Virus Modeling Space-warping molecular mechanics (MM) Tree code atomic force computations One billion grid node solutions of Poisson-Boltzmann equation (PB) MM/PB integration strategy Rigorous multiple scale modeling approaches Continuum models of the surrounding medium, lipid envelope, or host cell membrane can accelerate computations Viruses in droplets or on surfaces in context of contagion and disinfection analyses Stochastic dynamics based on rigorous multi-scale reduction of the classical mechanics problem Advanced Computational Methods for Supra-Million Atom Systems Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

VirusX Whole Virus Modeling: 

VirusX Whole Virus Modeling Poisson-Boltzmann predicted electrical potential on a 6853 grid for the 739,560 atom HRV capsid in a .15M ionic strength solution showing 10 kT/e potential levels indicated in dark/light grey. VirusX Poisson-Boltzmann Solution for HRV Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

VirusX Whole Virus Modeling: 

VirusX Whole Virus Modeling VirusX simulated structure of Poliovirus capsid involving 713,580 atoms. This energy-minimized structure shows atoms in CPK color coding. VirusX Molecular Mechanics Predicted Poliovirus Structure Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Vaccine Design: 

Vaccine Design Thousands of mutants are generated automatically and categorized by physico-chemical properties related to their stability and interaction with potential host cell and normal human anti-viral resistance processes. Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Drug Design Workflow: 

Drug Design Workflow Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Slide11: 

Dual Virus/Host Genomics Understanding resistance and susceptibility to viral infection at the whole genome level Center for Cell and Virus Theory Indiana University Bloomington IN 47405 ortoleva@indiana.edu biodynamics.indiana.edu Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Dual Virus/Host Genomics: 

Dual Virus/Host Genomics Microarrays on virus-free and infected human cells can provide insights into resistant versus susceptible cell lines and individuals. Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Dual Virus/Host Genomics: 

Dual Virus/Host Genomics Advanced elements developed at CCVT will be integrated to derive resistance, susceptibility and progression of disease information on infected human cell: KAGAN FTF Human cell regulatory database Interfaces with bioinformatics tools Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu

Dual Virus/Host Genomics: 

Dual Virus/Host Genomics Flowchart for discovering mechanisms of resistance and susceptibility to viral disease at the whole human genome level.   Center for Cell and Virus Theory  http://sysbio.indiana.edu  ortoleva@indiana.edu