Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model
TLDR
A fast fitting program, “gmfit”, which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models and was able to rebuild atomic models of a complex even for maps of 30 Å resolution if sufficient numbers of Gaussian distribution functions were employed for each subunit.About:
This article is published in Biophysical Journal.The article was published on 2008-11-15 and is currently open access. It has received 108 citations till now. The article focuses on the topics: Atomic model & Resolution (electron density).read more
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Integrative structure and functional anatomy of a nuclear pore complex
Seung Joong Kim,Javier Fernandez-Martinez,Ilona Nudelman,Yi Shi,Wenzhu Zhang,Barak Raveh,Thurston Herricks,Brian D. Slaughter,Joanna A. Hogan,Paula Upla,Ilan E. Chemmama,Riccardo Pellarin,Ignacia Echeverria,Manjunatha Shivaraju,Azraa S. Chaudhury,Junjie Wang,Rosemary Williams,Jay R. Unruh,Charles H. Greenberg,Erica Y. Jacobs,Zhiheng Yu,M. Jason de la Cruz,Roxana Mironska,David L. Stokes,John D. Aitchison,John D. Aitchison,Martin F. Jarrold,Jennifer L. Gerton,Steven J. Ludtke,Christopher W. Akey,Brian T. Chait,Andrej Sali,Michael P. Rout +32 more
TL;DR: The structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae is determined at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents.
Journal ArticleDOI
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly.
TL;DR: MultiFit is described, a method used for simultaneously fitting atomic structures of components into their assembly density map at resolutions as low as 25 A and can provide initial configurations for further refinement of many multicomponent assembly structures described by electron microscopy.
Journal ArticleDOI
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
Akira R. Kinjo,Gert-Jan Bekker,Hirofumi Suzuki,Yuko Tsuchiya,Takeshi Kawabata,Yasuyo Ikegawa,Haruki Nakamura +6 more
TL;DR: The updated web user interfaces together with RESTful web services and the backend relational database that support the former are outlined and enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources.
Journal ArticleDOI
Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.
Ashutosh Kumar,Kam Y. J. Zhang +1 more
TL;DR: This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Two distinct trimeric conformations of natively membrane-anchored full-length herpes simplex virus 1 glycoprotein B.
Tzviya Zeev-Ben-Mordehai,Daven Vasishtan,Anna Hernández Durán,Anna Hernández Durán,Benjamin Vollmer,Paul White,Arun Prasad Pandurangan,C. Alistair Siebert,Maya Topf,Kay Grünewald +9 more
TL;DR: In this paper, the authors characterized the full-length herpes simplex virus 1 gB in a native membrane by displaying it on cell-derived vesicles and using electron cryotomography.
References
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Book
Finite Mixture Models
Geoffrey J. McLachlan,David Peel +1 more
TL;DR: The important role of finite mixture models in the statistical analysis of data is underscored by the ever-increasing rate at which articles on mixture applications appear in the mathematical and statistical literature.
Posted Content
Finite Mixture Models
TL;DR: Finite mixture models as mentioned in this paper provide a natural way of modeling continuous or discrete outcomes that are observed from populations consisting of a finite number of homogeneous subpopulations, which are abundant in the social and behavioral sciences, biological and environmental sciences, engineering and finance.
Journal ArticleDOI
Comparative assessment of large-scale data sets of protein-protein interactions.
Christian von Mering,Roland Krause,Berend Snel,Michael Cornell,Stephen G. Oliver,Stanley Fields,Peer Bork +6 more
TL;DR: Comprehensive protein–protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function and are compared with each other and with a reference set of previously reported protein interactions.
Journal ArticleDOI
Proteomics to study genes and genomes
TL;DR: Proteomics can be divided into three main areas: protein micro-characterization for large-scale identification of proteins and their post-translational modifications; ‘differential display’ proteomics for comparison of protein levels with potential application in a wide range of diseases; and studies of protein–protein interactions using techniques such as mass spectrometry or the yeast two-hybrid system.
Journal ArticleDOI
The crystal structure of the asymmetric GroEL–GroES–(ADP) 7 chaperonin complex
TL;DR: The structure of the GroEL–GroES–(ADP)7 complex reveals how large en bloc movements of the cis ring's intermediate and apical domains enable bound GroES to stabilize a folding chamber with ADP confined to the cisRing, suggesting a model for an ATP-driven folding cycle that requires a double toroid.