Harper Wood

A strategy to validate protein function predictions in vitro

Prachee Avasthi, Brae M. Bigge, Atanas Radkov, Harper Wood, and Ryan York

Published: May 31, 2024

We aim to validate ProteinCartography, a tool for structure-based protein clustering, by evaluating two foundational hypotheses: that proteins within a cluster have similar functions and proteins in different clusters have differing functions.

Connections

Replies (2): How can we biochemically validate protein function predictions with the deoxycytidine kinase family? • How can we biochemically validate protein function predictions with the Ras GTPase family?

Supplements (2): Associated data - Zenodo • Previous ProteinCartography results - Zenodo

How can we biochemically validate protein function predictions with the deoxycytidine kinase family?

Prachee Avasthi, Brae M. Bigge, Atanas Radkov, Harper Wood, and Ryan York

Published: May 31, 2024

The human deoxycytidine kinase, a member of the nucleoside salvage pathway, has been studied extensively. We’ll use this family to assess our structure-based protein clustering tool, ProteinCartography. We’d love feedback on how we might work with this protein for validation.

Connections

Supplements (1): Data - Zenodo

How can we biochemically validate protein function predictions with the Ras GTPase family?

Prachee Avasthi, Brae M. Bigge, Atanas Radkov, Harper Wood, and Ryan York

Published: May 31, 2024

We’re using the well-studied superfamily of small monomeric GTPases, the Ras GTPases, to evaluate our structure-based clustering tool, ProteinCartography. We’re seeking feedback on working with this protein family and determining which individual proteins to study.

Connections

Supplements (1): Data - Zenodo