In a new paper, researchers at IBM Research recently presented a novel approach to retrosynthesis. In chemical synthesis, the retrosynthesis problem involves determining the optimal sequence of steps to synthesize a given molecule starting from readily available building blocks, known as precursors. In retrosynthesis, a chemist or computational model must first identify a suitable disconnection […]
Molecular docking is a critical task in drug design, as it involves predicting the binding structure of a small molecule ligand to a protein. Traditional methods for molecular docking rely on search-based algorithms and scoring functions to estimate the correctness of a proposed structure. However, these methods can be slow and inaccurate, especially for high-throughput […]
RFDiffusion is a new method for protein design that leverages the power of denoising diffusion probabilistic models (DDPMs) to generate protein sequences and protein structures. This approach represents a significant advance in the field of protein design, as it allows for the design of complex protein architectures and functions from simple molecular specifications. Figure 1: RFDiffusion […]
Molecular docking tools are commonly used in drug discovery to computationally identify new molecules through virtual screening. However, these tools often suffer from inaccurate scoring functions that can vary in performance across different proteins. To address this issue, researchers at Brigham Young University have developed MILCDock, a machine learning consensus docking tool that uses predictions from […]
I thoroughly enjoyed meeting Andreas Bender at the recent BioTechX conference in Basel. He gave a very honest and thought-provoking presentation on a series of papers released in Drug Discovery Today, titled: Artificial intelligence in drug discovery: what is realistic, what are illusions? Let’s recap his main findings: Artificial intelligence (AI) has had a profound impact on many areas […]
In the past two months, DALL·E 2 has taken over the internet. From Bart Simpson edited into Egyptian art to Donald Trump as the Lorax, text-to-image AI produces amazing results. Caption: “Panda weaving a basket made of cyclohexane”, DALL·E 2 Are these an impressive-but-gimmicky party trick? Or can these innovations be harnessed for applications in scientific domains? Many […]
The history of chemistry has been epitomized by individual chemists coming up with hypotheses, running experiments at lab-scale, and producing discoveries. But in 2022, chemistry data is generated at a scale previously unseen, computers can rapidly process that data, and the data can be widely distributed at relatively minimal cost. This new frontier of global-scale […]
In drug discovery, there are two main approaches to hit finding: 1) virtual screening of existing small molecule libraries and 2) generative design of new molecules. Generative molecule design can result in better binders, but it may be unknown how to synthesize them. The task of retrosynthesis – designing a synthesis pathway for a molecule […]
Many of our recent blog posts have dealt with physical modeling of small molecules and proteins. This is due to a recent flurry of groundbreaking research in equivariant neural networks that have improved structural modeling of chemicals. But today we step back to a broader-scope biochemistry problem. We are reviewing a paper from a few years ago, […]