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• W4321330245 abstract "ABSTRACT Sequence assignment is a key step of the model building process in both cryogenic electron microscopy (cryo-EM) and macromolecular crystallography (MX). If the assignment fails, it can result in difficult to identify errors affecting the interpretation of a model. There are many model validation strategies that help experimentalists in this step of protein model building, but they are virtually non-existent for nucleic acids. Here I present doubleHelix – a comprehensive method for assignment, identification, and validation of nucleic acid sequences in structures determined using cryo-EM and MX. The method combines a neural network classifier of nucleobase identities and a sequence-independent secondary structure assignment approach. I show that the presented method can successfully assist model building at lower resolutions, where visual map interpretation is very difficult. Moreover, I present examples of sequence assignment errors detected using doubleHelix in cryo-EM and MX structures of ribosomes deposited in the Protein Data Bank, which escaped the scrutiny of available model-validation approaches. The doubleHelix program source code is available under BSD-3 license at https://gitlab.com/gchojnowski/doublehelix ." @default.
• W4321330245 created "2023-02-19" @default.
• W4321330245 creator A5020340417 @default.
• W4321330245 date "2023-02-17" @default.
• W4321330245 modified "2023-09-25" @default.
• W4321330245 title "doubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models" @default.
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• W4321330245 doi "https://doi.org/10.1101/2023.02.17.528963" @default.
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