B2I-Tools

DeepSSETracer SSETracer StrandTwister AxisComparison BundleTrac

Tools for Detection and Evaluation of Secondary Structures from Cryo-EM Maps of the Medium-Resolution

Biomolecular and Biomedical Informatics Lab (B2I)

Computer Science Department of Old Dominion University

DeepSSETracer

DeepSSETracer is a tool that uses a trained CNN model to detect helices and beta-sheets from a cryo-EM map of medium resolution (5-10 Å).

DeepSSETracer Image

Reference:

Mu, Y.; Nguyen, T.; Hawickhorst, B.; Wriggers, W.; Sun, J.; He, J. "The combined focal loss and dice loss function improves the segmentation of beta-sheets in medium-resolution cryo-electron-microscopy density map", Bioinformatics Advances, 2024, (accepted).

SSETracer

SSETracer is a tool and an algorithm for detecting secondary structures in cryo-EM maps of medium resolution.

SSETracer Image

Reference:

Si, D.; He, J. "Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps", Proceeding of ACM Conference on Bioinformatics Computational Biology and Biomedicine Workshops, Washington, D.C., September 22-25, 2013.

StrandTwister

StrandTwister is a tool for estimation of beta strand locations from segmented beta-sheets.

StrandTwister Image

Reference:

Si, D.; He, J. "Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolution", Structure, 22(11):1665-76, 2014.

AxisComparison

AxisComparison is a tool for evaluating the accuracy of detected helices and beta strands in lateral and longitudinal error.

AxisComparison Image

Reference:

Zeil, S.; Kovacs, J.; Wriggers, W., He, J. "Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix", Journal of Computational Biology, 24(1), 52-67, 2017.

BundleTrac

BundleTrac helps analyze the structural arrangement of bundles and loops in cryo-EM maps.

BundleTrac Image

Reference:

Sazzed, S.; Song, J.; Kovacs, J.A.; Wriggers, W.; Auer, M.; He, J. Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia. Molecules 2018, 23, 882.