Quantification of Density Fit of Atomic Model to Helices in 3D Cryo-Electron Microscopy Images
Description/Abstract/Artist Statement
Cryo-electron microscopy density maps at medium resolutions (5-10Å) offer insights about secondary structures, such as α-helices and β-sheets. However, they lack the density characteristics of side chains that are important in structure determination. Among over 800 entries of medium-resolution density maps linked to atomic models in the Electron Microscopy Data Bank (EMDB), various levels of fit have been observed previously. We propose a measure of cylindrical agreement between the density and atomic model of a helix for medium-resolution density maps. An analysis of 30,994 helices in 3,247 protein chains with both medium-resolution density maps and atomic models shows a wide range of F1 scores from 0.171 to 0.848. The results indicate a tendency for the density distribution around a helix to deviate from the cylindrical shape expected by the model when the F1 score is below 0.55.
Faculty Advisor/Mentor
Jing He
Presentation Type
Poster
Disciplines
Bioinformatics | Structural Biology | Theory and Algorithms
Session Title
Poster Session
Location
Learning Commons, Atrium
Start Date
2-8-2020 8:00 AM
End Date
2-8-2020 12:30 PM
Quantification of Density Fit of Atomic Model to Helices in 3D Cryo-Electron Microscopy Images
Learning Commons, Atrium
Cryo-electron microscopy density maps at medium resolutions (5-10Å) offer insights about secondary structures, such as α-helices and β-sheets. However, they lack the density characteristics of side chains that are important in structure determination. Among over 800 entries of medium-resolution density maps linked to atomic models in the Electron Microscopy Data Bank (EMDB), various levels of fit have been observed previously. We propose a measure of cylindrical agreement between the density and atomic model of a helix for medium-resolution density maps. An analysis of 30,994 helices in 3,247 protein chains with both medium-resolution density maps and atomic models shows a wide range of F1 scores from 0.171 to 0.848. The results indicate a tendency for the density distribution around a helix to deviate from the cylindrical shape expected by the model when the F1 score is below 0.55.