MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and
model organism Zea mays.
MaizeGDB is a founding member of
AgBioData,
a consortuim of agriculture-related online resources which is
committed to making agriculture-related research data FAIR.
TYPSimSelector: A tool that sorts identity-by-state values derived from SNP datasets for accessions in the Ames Diversity Panel (a USDA-maintained set of maize lines representing wide genetic variation in Ames, Iowa).
GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
Foldseek is a free and open-source program that enables fast and sensitive comparisons of large structure sets. MaizeGDB used foldseek to align the 39,299 AlphaFold predicted protein structure from maize against eight proteomes: Arabidopsis thaliana (Arabidopsis), Glycine max (Soybean), Oryza sativa (Asian rice) and Zea mays (Maize), Homo sapiens (Human), Saccharomyces cerevisiae (Budding yeast), Schizosaccharomyces pombe (Fission yeast), and Sorghum bicolor (Sorghum). Try searching your gene or protein of interest in the box below!
FATCAT Comparison
This tool shows the structural alignments between a query maize protein with the top hits from the sequence-based tool Diamond and two structural alignment tools FoldSeek and FATCAT. Each of the 39,299 AlphaFold predicted protein structures from maize was aligned against the following four plant proteomes: Arabidopsis thaliana (Arabidopsis), Glycine max (Soybean), Oryza sativa (Asian rice), and Sorghum bicolor (Sorghum). The protein structure models are from version 3 released in July 2022. Try searching your gene or protein of interest in the box below!
EMBL-EBI AlphaFold Protein Structures
AlphaFold is an artificial intelligence system by DeepMind (reference), and was used to create predictions of maize protein structures based on the B73 RefGen_v4 gene model protein sequences. Enter a gene or protein below to view the predicted AlphaFold structure.
The protein structure is color-coded based on per-residue confidence scores (pLDDT):
Very high (avg pLDDT > 90) Confident (70 < avg pLDDT < 90) Low (50 < avg pLDDT < 70) Very low (avg pLDDT < 50)
The AlphaFold track shows B73 RefGen_v4 gene model CDS transcript annotations mapped to the B73 RefGen_v5 genome with each exon color-coded (using the same key described above) based on Deepmind's AlphaFold predicted protein structure scores.
MetaAI ESMFold Protein Structures
ESMFold is an artificial intelligence system by MetaAI (reference), and was used to create predictions of maize protein structures based on the Zm-B73-REFERENCE-NAM-5.0 gene model protein sequences. Enter a gene or protein below to view the predicted ESMFold structure.
The protein structure is color-coded based on per-residue confidence scores (pLDDT):
Very high (avg pLDDT > 90) Confident (70 < avg pLDDT < 90) Low (50 < avg pLDDT < 70) Very low (avg pLDDT < 50)
The ESMFold track shows B73 RefGen_v5 gene model CDS transcript annotations (71,725 isoforms) with each exon color-coded (using the same key described above) based on MetaAI's ESMFold predicted protein structure scores.
