BindCraft is a revolutionary open-source AI platform that is democratizing protein design. It democratizes the use of advanced biotechnological tools to a greater extent than ever, reaching more laboratories and researchers. The Technology A team of scientists from the Laboratory of Protein Design and Immunoengineering (LPDI) at the École Polytechnique Fédérale de Lausanne (EPFL) created this revolutionary platform. They described their results in a research article in the journal Nature, which was accessed via Phys.org on August 29, 2023.
BindCraft will allow users—from academic labs to pharmaceutical companies—to design new protein binders that can more efficiently and precisely unlock biological functions. Bruno Correia, who heads up their research team, and meanwhile, they’ve made a really exciting breakthrough. Their binders have seriously stuck to the right targets too, with a nasty average success rate of 46%! This major milestone further illustrates the power of the platform. It further underscores the precautionary approach that we argued should apply to gene editing and similar technologies.
Martin Pacesa, the first author of this study, is a scientist at LPDI. He explained further about the remarkable strength that the binders created in the BindCraft process. These binders can inhibit the gene-editing activity of CRISPR-Cas9, stopping it from working in unwanted cells or tissues.
“For AAVs, the idea is to use these new binders to enable gene delivery only to specific cells and tissues while minimizing the risk of potential side effects. In the case of CRISPR-Cas9, our binders can stop its gene editing activity and keep it from acting when and where it shouldn’t.” – Martin Pacesa
Lennart Nickel, Ph.D. student at LPDI, explained how BindCraft’s approach is superior to binder discovery techniques used in the past. He noted that conventional approaches sometimes require high levels of experimental expertise. Not every research team has the computational expertise to fulfill those requirements.
“Traditional binder discovery methods involve screening tens of thousands of protein candidates, which requires experimental capabilities and computational expertise that not every lab can afford or has.” – Lennart Nickel
The creation of BindCraft is an exciting next step in our efforts to make protein design more approachable. Catholic Relief Services’ Christian Schellhaas, another member of the development team, described how the platform makes the binder discovery process much more efficient.
“With BindCraft, we essentially reverse-engineer the current pipeline by using the protein structure prediction network right from the start to generate novel binders that have the properties we’re looking for.” – Christian Schellhaas
The overwhelming acceptance and rapid adoption of BindCraft in both academic and industrial settings have surpassed the team’s expectations and imagination. Pacesa was quick to add that user feedback and requests have served as a muse for continued development since launch.
“We were surprised by how quickly our tool has been adopted—it is even already being used in industry. The requests from users are a great inspiration to continue developing our method. We are already working on adapting BindCraft for smaller therapeutically relevant molecules like peptides.” – Martin Pacesa