Referenced Papers (4)
Computational Design of Metallohydrolases
Donghyo Kim, Seth M Woodbury, Woody Ahern, D Tischer, Nikita Hanikel, Saman Salike
bioRxiv, 2025
"This paper is cited as an example of designing a 'theozyme' (a theoretical enzyme active site) for a novel chemical reaction using Density Functional Theory (DFT) calculations."
Computational design of serine hydrolases
Anna Lauko, S Pellock, Ivan Anischanka, K Sumida, David Juergens, Woody Ahern
bioRxiv, 2024
"This paper is referenced to highlight the inefficiencies and very low in silico success rates of current de novo enzyme design campaigns, using the design of serine hydrolases as an example."
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 paper on the original RFdiffusion model is cited to illustrate the challenges of using backbone-resolution methods for enzyme design, as they often fail to create proper pockets for ligands."
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 introduces RFdiffusion All-Atom, an atomic-level generative model that enables the design of various biomolecules, setting the stage for more complex tasks like enzyme design."