Referenced Papers (6)
Unraveling the functional dark matter through global metagenomics
Georgios A Pavlopoulos, Fotis A Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach
Nature, 2023
"This paper is cited to support the claim that current biological knowledge has only scratched the surface of sequence diversity, especially in metagenomes where new protein sequence clusters are discovered exponentially with more samples."
Exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm
Teng-Yu Lin, Szu-Chi Chung
bioRxiv, 2023
"This citation is used to illustrate that while protein structure prediction has made great strides (like with ESMFold/AlphaFold2), knowing the structure alone does not directly reveal a protein's function."
Convergent evolution of enzyme active sites is not a rare phenomenon
Pier Federico Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J E Sternberg
J. Mol. Biol., 2007
"This paper is cited to demonstrate that protein function is not solely determined by structure, as similar structures can have different functions, and different structures can have identical functions, indicating convergent evolution of active sites."
Genomic language model predicts protein co-regulation and function
Yunha Hwang, Andre L Cornman, Elizabeth H Kellogg, Sergey Ovchinnikov, Peter R Girguis
Nat. Commun., 2024
"This is the speaker's own recently published work, introducing the concept of a genomic language model (gLM) that predicts protein co-regulation and function by learning patterns in genomes."
Protein language models are biased by unequal sequence sampling across the tree of life
Frances Ding, Jacob Steinhardt
bioRxiv, 2024
"This paper is cited to highlight the problem of bias in protein sequence datasets, where sampling is unequal across the tree of life, which can impact the generalizability of foundation models."
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
Wei Liu, Ziye Wang, R You, Chenghan Xie, Hong Wei, Yi Xiong
Nat. Commun., 2024
"This paper introduces PLMSearch, a method that uses protein language models for accurate and fast sequence search for remote homology, providing inspiration for the speaker's gLMSearch concept."