Pictorial Structures for Molecular Modeling: Interpreting Density Maps

Part of Advances in Neural Information Processing Systems 17 (NIPS 2004)

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Frank Dimaio, George Phillips, Jude Shavlik


X-ray crystallography is currently the most common way protein structures are elucidated. One of the most time-consuming steps in the crystallographic process is interpretation of the electron density map, a task that involves finding patterns in a three-dimensional picture of a protein. This paper describes DEFT (DEFormable Template), an algorithm using pictorial structures to build a flexible protein model from the protein's amino-acid sequence. Matching this pictorial structure into the density map is a way of automating density-map interpretation. Also described are several extensions to the pictorial structure matching algorithm necessary for this automated interpretation. DEFT is tested on a set of density maps ranging from 2 to 4Å resolution, producing root- mean-squared errors ranging from 1.38 to 1.84Å.