Proteingym: Large-scale benchmarks for protein fitness prediction and design
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …
understanding genetic disease to designing novel proteins to address our most pressing …
Proteinnpt: Improving protein property prediction and design with non-parametric transformers
Protein design holds immense potential for optimizing naturally occurring proteins, with
broad applications in drug discovery, material design, and sustainability. However …
broad applications in drug discovery, material design, and sustainability. However …
Ancestral reconstruction and the evolution of protein energy landscapes
A protein's sequence determines its conformational energy landscape. This, in turn,
determines the protein's function. Understanding the evolution of new protein functions …
determines the protein's function. Understanding the evolution of new protein functions …
[HTML][HTML] Rheostats, toggles, and neutrals, Oh my! A new framework for understanding how amino acid changes modulate protein function.
L Swint-Kruse, AW Fenton - Journal of Biological Chemistry, 2024 - Elsevier
Advances in personalized medicine and protein engineering require accurately predicting
outcomes of amino acid substitutions. Many algorithms correctly predict that evolutionarily …
outcomes of amino acid substitutions. Many algorithms correctly predict that evolutionarily …
[HTML][HTML] Proteingym: Large-scale benchmarks for protein design and fitness prediction
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins that can address our most …
understanding genetic disease to designing novel proteins that can address our most …
Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain
GO Estevam, EM Linossi, CB Macdonald, CA Espinoza… - Elife, 2024 - elifesciences.org
MET is a receptor tyrosine kinase (RTK) responsible for initiating signaling pathways
involved in development and wound repair. MET activation relies on ligand binding to the …
involved in development and wound repair. MET activation relies on ligand binding to the …
High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display
Tyrosine kinases and SH2 (phosphotyrosine recognition) domains have binding specificities
that depend on the amino acid sequence surrounding the target (phospho) tyrosine residue …
that depend on the amino acid sequence surrounding the target (phospho) tyrosine residue …
Allosteric modulation of NF1 GAP: Differential distributions of catalytically competent populations in loss‐of‐function and gain‐of‐function mutants
Abstract Neurofibromin (NF1), a Ras GTPase‐activating protein (GAP), catalyzes Ras‐
mediated GTP hydrolysis and thereby negatively regulates the Ras/MAPK pathway. NF1 …
mediated GTP hydrolysis and thereby negatively regulates the Ras/MAPK pathway. NF1 …
Large language models for biological prediction and design
AW Kollasch - 2023 - search.proquest.com
Predicting the functional impact of changes to biological sequences is a central challenge in
genetics and biology. Beyond genetics, sequence-to-function map** has key applications …
genetics and biology. Beyond genetics, sequence-to-function map** has key applications …
Deep generative models for biology: represent, predict, design
P Notin - 2023 - ora.ox.ac.uk
Deep generative models have revolutionized the field of artificial intelligence, fundamentally
changing how we generate novel objects that imitate or extrapolate from training data, and …
changing how we generate novel objects that imitate or extrapolate from training data, and …