Thursday, April 10th at 11:00am EST -- please join our webinar to hear Matt Baker, Instructor at Baylor College of Medicine, give an introduction to Modeling Macromolecular Structures with Gorgon.
Matt Baker, Ph.D.
Instructor, Department of Biochemistry and Molecular Biology,
Baylor College of Medicine
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, is critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution.To this end, we developed a new interactive toolkit (Gorgon) for modeling intermediate resolution density maps (10-3.5 Å), particularly from cryo-EM. To date, Gorgon offers a unique approach to model building not found in any other molecular modeling toolkit. Primarily built around a novel de novo modeling procedure that couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques, initial protein backbone models for individual components of macromolecular assemblies can be constructed rapidly with high fidelity using Gorgon's interactive environment. To further facilitate interoperation with other protein modeling software, Gorgon was also designed as an extensible interactive platform, bridging intermediate and high-resolution structure discovery.
For more information on Gorgon software, check out the Gorgon website or read one of these papers of interest:
- Baker ML, Baker MR, Hryc CF, Ju T, Chiu W. Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers. 2012 Sep;97(9):655-68. doi: 10.1002/bip.22065. PubMed PMID: 22696403; PubMed Central PMCID: PMC3899894. Abstract
- Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. Modeling protein structure at near atomic resolutions with Gorgon. J Struct Biol. 2011 May;174(2):360-73. doi: 10.1016/j.jsb.2011.01.015. Epub 2011 Feb 4. PubMed PMID: 21296162; PubMed Central PMCID: PMC3078171. Abstract
- Abeysinghe S, Baker ML, Chiu W, Ju T. Semi-isometric registration of line features for flexible fitting of protein structures. Comput Graph Forum. 2010;29(7):2243-2252. PubMed PMID: 21124809; PubMed Central PMCID: PMC2993115. Abstract
- Ju T, Baker ML, Chiu W. Computing a family of skeletons of volumetric models for shape description. Comput Aided Des. 2007 May;39(5):352-360. PubMed PMID: 18449328; PubMed Central PMCID: PMC2084352. Abstract
- Baker ML, Ju T, Chiu W. Identification of secondary structure elements in intermediate-resolution density maps. Structure. 2007 Jan;15(1):7-19. PubMed PMID: 17223528; PubMed Central PMCID: PMC1810566. Abstract
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