CryoEM and Comparative Modeling
19 March, 2007 - 1 min read
I read a great paper by Såli et al this week, Refining Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting.
I remember Matthew Baker, one of the authors on this paper, spoke at CASP7 last year. This is an exciting application of modeling since CryoEM can provide the structure of large virus assemblies and membranes. Where comparative modeling becomes important is increasing the resolution to pseudo- atom structures so you can really see what’s happening in terms of chemistry. With simulated electron density maps, Sali et al benchmarked a comparative modeling pipeline which added a density fit score to the DOPE potential.
The genetic algorithm runs for 15 hours on a 50 node dual-PIII cluster.