Maize protein structure resources at the maize genetics and genomics database

Authors: Woodhouse, Margaret; Portwood, John; SEN, SHATABDI - Iowa State University; HAYFORD, RITA - Orise Fellow; GARDINER, JACK - University Of Missouri; Cannon, Ethalinda; HARPER, LISA - Retired ARS Employee; Andorf, Carson

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2023
Publication Date: 2/9/2023
Citation: Woodhouse, M.H., Portwood II, J.L., Sen, S., Hayford, R.K., Gardiner, J.M., Cannon, E.K., Harper, L.C., Andorf, C.M. 2023. Maize protein structure resources at the maize genetics and genomics database. Genetics. 224(1).Article iyad016. https://doi.org/10.1093/genetics/iyad016.
DOI: https://doi.org/10.1093/genetics/iyad016

Interpretive Summary: Protein structures play an important role in biological research, such as in predicting the function of genes or evaluating gene structures. However, determining protein structure was, until now, highly time-consuming, inaccurate, and limited to the size of the protein, all of which resulted in a structural biology bottleneck. With the release of such programs AlphaFold and ESMFold, this bottleneck has been greatly reduced, permitting protein structure comparisons of entire genomes within reasonable timeframes. MaizeGDB has leveraged this technological breakthrough by offering several new tools to accelerate protein structure comparisons between maize and other species. MaizeGDB also offers bulk downloads of these protein structure data, along with predicted gene function information. In this way, MaizeGDB is poised to assist maize researchers in assessing protein structure and function with data unavailable to maize scientists even a few years ago.

Technical Abstract: Protein structures play an important role in bioinformatics, such as in predicting gene function or validating gene model annotation. However, determining protein structure was, until now, highly time-consuming, inaccurate, and limited to the size of the protein, all of which resulted in a structural biology bottleneck. With the release of such programs AlphaFold and ESMFold, this bottleneck has been reduced by several orders of magnitude, permitting protein structural comparisons of entire genomes within reasonable timeframes. MaizeGDB has leveraged this technological breakthrough by offering several new tools to accelerate protein structural comparisons between maize and other plants as well as human and yeast outgroups. MaizeGDB also offers bulk downloads of these comparative protein structure data, along with predicted functional annotation information. In this way, MaizeGDB is poised to assist maize researchers in assessing functional homology, gene model annotation quality, and other information unavailable to maize scientists even a few years ago.