Foundation models for generalist medical artificial intelligence

M Moor, O Banerjee, ZSH Abad, HM Krumholz… - Nature, 2023 - nature.com
The exceptionally rapid development of highly flexible, reusable artificial intelligence (AI)
models is likely to usher in newfound capabilities in medicine. We propose a new paradigm …

Modeling conformational states of proteins with AlphaFold

D Sala, F Engelberger, HS Mchaourab… - Current Opinion in …, 2023 - Elsevier
Many proteins exert their function by switching among different structures. Knowing the
conformational ensembles affiliated with these states is critical to elucidate key mechanistic …

Protein structure generation via folding diffusion

KE Wu, KK Yang, R van den Berg, S Alamdari… - Nature …, 2024 - nature.com
The ability to computationally generate novel yet physically foldable protein structures could
lead to new biological discoveries and new treatments targeting yet incurable diseases …

Protein design with guided discrete diffusion

N Gruver, S Stanton, N Frey… - Advances in neural …, 2024 - proceedings.neurips.cc
A popular approach to protein design is to combine a generative model with a discriminative
model for conditional sampling. The generative model samples plausible sequences while …

Improving de novo protein binder design with deep learning

NR Bennett, B Coventry, I Goreshnik, B Huang… - Nature …, 2023 - nature.com
Recently it has become possible to de novo design high affinity protein binding proteins from
target structural information alone. There is, however, considerable room for improvement as …

Riemannian score-based generative modelling

V De Bortoli, E Mathieu, M Hutchinson… - Advances in …, 2022 - proceedings.neurips.cc
Score-based generative models (SGMs) are a powerful class of generative models that
exhibit remarkable empirical performance. Score-based generative modelling (SGM) …

SE (3) diffusion model with application to protein backbone generation

J Yim, BL Trippe, V De Bortoli, E Mathieu… - arXiv preprint arXiv …, 2023 - arxiv.org
The design of novel protein structures remains a challenge in protein engineering for
applications across biomedicine and chemistry. In this line of work, a diffusion model over …

AbDiffuser: full-atom generation of in-vitro functioning antibodies

K Martinkus, J Ludwiczak, WC Liang… - Advances in …, 2024 - proceedings.neurips.cc
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …

From nature to industry: Harnessing enzymes for biocatalysis

R Buller, S Lutz, RJ Kazlauskas, R Snajdrova… - Science, 2023 - science.org
Biocatalysis harnesses enzymes to make valuable products. This green technology is used
in countless applications from bench scale to industrial production and allows practitioners …

Computational and artificial intelligence-based methods for antibody development

J Kim, M McFee, Q Fang, O Abdin, PM Kim - Trends in pharmacological …, 2023 - cell.com
Due to their high target specificity and binding affinity, therapeutic antibodies are currently
the largest class of biotherapeutics. The traditional largely empirical antibody development …