Referenced Papers (4)
Computational Design of Metallohydrolases
Donghyo Kim, Seth M Woodbury, Woody Ahern, D Tischer, Nikita Hanikel, Saman Salike
bioRxiv, 2025
"The speaker uses this recent preprint, which they co-authored, as an example of designing theozymes for novel chemistries using DFT calculations."
Computational design of serine hydrolases
Anna Lauko, S Pellock, K Sumida, Ivan Anishchenko, David Juergens, Woody Ahern
Science, 2025
"This paper is cited to illustrate the inefficiencies in de novo enzyme design, highlighting the low in silico filter success rate and the gap between designed and native catalytic efficiency."
De novo design of protein structure and function with RFdiffusion
Joseph L Watson, David Juergens, N Bennett, Brian L Trippe, Jason Yim, Helen E Eisenach
Nature, 2023
"This is the original RFdiffusion paper, cited to discuss its limitations for enzyme design, such as its inability to create tight binding pockets or avoid clashes with substrates."
Generalized biomolecular modeling and design with RoseTTAFold All-Atom
Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet
bioRxiv, 2023
"This paper on RosettaFold All-Atom is cited as a recent advancement in all-atom generative models, which paves the way for the all-atom design approach discussed in the talk."