Title

Quantification of Density Fit of Atomic Model to Helices in 3D Cryo-Electron Microscopy Images

Description/Abstract

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.

Presenting Author Name/s

Peter Scheible

Faculty Advisor

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

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Feb 8th, 8:00 AM Feb 8th, 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.