Unknown

Dataset Information

0

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.

SUBMITTER: Baker ML 

PROVIDER: S-EPMC3078171 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature

altmetric image

Publications

Modeling protein structure at near atomic resolutions with Gorgon.

Baker Matthew L ML   Abeysinghe Sasakthi S SS   Schuh Stephen S   Coleman Ross A RA   Abrams Austin A   Marsh Michael P MP   Hryc Corey F CF   Ruths Troy T   Chiu Wah W   Ju Tao T  

Journal of structural biology 20110204 2


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  ...[more]

Similar Datasets

| S-EPMC3954858 | biostudies-literature
| S-EPMC3725109 | biostudies-literature
| S-EPMC4435692 | biostudies-literature
| S-EPMC6344570 | biostudies-literature
| S-EPMC4493910 | biostudies-literature
| S-EPMC4588362 | biostudies-literature
| S-EPMC5050015 | biostudies-literature
| S-EPMC8439582 | biostudies-literature
| S-EPMC11217428 | biostudies-literature
| S-EPMC5003279 | biostudies-literature