DoubleHelix: nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.
Nucleic Acids Res
; 51(15): 8255-8269, 2023 08 25.
Article
em En
| MEDLINE
| ID: mdl-37395405
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 sequence-assignment step in nucleic-acid 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.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Ácidos Nucleicos
Tipo de estudo:
Diagnostic_studies
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article