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Modeling protein structure at near atomic resolutions with Gorgon

2011; Elsevier BV; Volume: 174; Issue: 2 Linguagem: Inglês

10.1016/j.jsb.2011.01.015

1095-8657

Matthew L. Baker, Sasakthi S. Abeysinghe, Stephen Schuh, Ross A. Coleman, Austin Abrams, Michael P. Marsh, Corey F. Hryc, Troy Ruths, Wah Chiu, Tao Ju,

Photosynthetic Processes and Mechanisms

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10–3.5 Å), particularly from cryo-EM. Gorgon’s de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure.