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  Title:   General Automated Atomic Model Parameterization  
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  Coverage:   November 18, 2016 - November 18, 2016  
  Description:   One of the key concepts in the design of the present Consortium is out ability to rationalize through computational means a vast amount of static and dynamics structural data with functional information. The computational Core is designed to generate, implement, validate and distribute state-of-the-art “tools” required for the studies of complex membrane protein systems. This includes expertise and services of well-established tools, novel methods and technologies that will support the experimental studies, such as methods for analysis of spectroscopic data, and ground work on basic computational staples like force fields and biomolecular simulations. All the computational methodologies will be readily made available to the broader scientific community through our website. From the outset, Cores will have pre-set interactions with the different projects as depicted in Figure 4. By design, two Cores will necessarily have a direct impact in the development of all bridging (and pilot) projects. These are Core D1 (Protein expression and purification), which will have a hand in securing purified material and mutants for biophysical measurements and functional reconstitution, and Core D4 (Computational and Modeling resource), which will help to put into mechanistic and energetic perspective the vast amounts of data we expect to collect. Roux, Bahar, Schulten, Tajkhorshid, Weinstein   Figure Caption: Pseudo-atoms representing the spin label attached to each residue, are shown for one subunit and color coded as follows: red particles represent buried residues, blue cles represent aqueous residues, yellow particles represent residues facing the membrane, and green particles represent residues at the water-membrane interface. Red les are shown for each Cα atom representing PROT particles attached to each residue. Inset shows protein residues in thin licorice representation and pseudospin probes in  CPK representation. Unbounded particles in red and blue represent O2 and NiEdda virtual environment particles, respectively. View of the NH2-terminal model after pseudoatom-driven solvent accessibility refinement is shown on the right panel. Residues 1 to 28 are shown in gray; resultant vectors for NiEdda and O2 accessibilities are shown in blue and red, respectively. Taken from Vasquez et al.  J Mol Biol 378:55-70, 2008).