Gilad Mishne

ProteinCartography: Comparing proteins with structure-based maps for interactive exploration

Prachee Avasthi, Brae M. Bigge, Feridun Mert Celebi, Keith Cheveralls, Jase Gehring, Erin McGeever, Gilad Mishne, Atanas Radkov, and 1 more

Published: Sep 29, 2023

The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.

Connections

Supplements (3): ProteinCartography v0.5.0 - GitHub • ProteinCartography v0.4.2 - GitHub • Data - Zenodo

Using protein language models to predict coding and non-coding transcripts with plm-utils

Adair L. Borges, Feridun Mert Celebi, Keith Cheveralls, and Taylor Reiter

Published: Aug 08, 2024

We explored the use of embeddings from protein language models to distinguish between genuine and putative coding open reading frames (ORFs). We found that an embeddings-based approach (shared as a small Python package called plm-utils) improves identification of short ORFs.

Connections

Supplements (2): Code v1.0.0 - GitHub • Evaluation and training code - GitHub