title: Modeling protein structure at near atomic resolutions with Gorgon.
abstract: 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.
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. mbaker@bcm.edu
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Baker
authors.forename: Sasakthi S
authors.initials: SS
authors.lastname: Abeysinghe
authors.forename: Stephen
authors.initials: S
authors.lastname: Schuh
authors.forename: Ross A
authors.initials: RA
authors.lastname: Coleman
authors.forename: Austin
authors.initials: A
authors.lastname: Abrams
authors.forename: Michael P
authors.initials: MP
authors.lastname: Marsh
authors.forename: Corey F
authors.initials: CF
authors.lastname: Hryc
authors.forename: Troy
authors.initials: T
authors.lastname: Ruths
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
authors.forename: Tao
authors.initials: T
authors.lastname: Ju
mesh_terms: D000595:Amino Acid Sequence; D000956:Antigens, Viral / Q000737:chemistry; D036022:Capsid Proteins / Q000737:chemistry; D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000379:methods; D003626:Data Display; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D000956:Antigens, Viral; D036022:Capsid Proteins; D011506:Proteins; C061332:VP6 protein, Rotavirus