Peptone
Accelerating protein-based drug discovery using computational molecular physics
Published 26 APR 2022
Protein structures and their various conformations are dynamic and complex. Proteins such as receptors, antibodies, growth factors, and hormones have a vast number of potential variations in structure and their molecular behaviour can be varied. Proteins can aggregate, or stick together, altering their characteristics, and one protein’s interaction with another can change its shape and functionality. Understanding how proteins act, knowing their size, and visualising how they look is a fundamental key to creating protein-based drugs and vaccines.
UK-headquartered Peptone is at the forefront of this research, in partnership with NVIDIA and Verne Global datacentres. Peptone is a computational molecular physics company that has used artificial intelligence methods to analyse the anomalous behaviour of proteins and has developed the Protein Engineering Operating System (PeOS).
Developing the PeOS
Peptone’s team of physicists, structural biologists, computer engineers and mathematicians, led by physicist and founder Dr Kamil Tamiola, has spent the last three years developing the foundations of Protein Engineering Operating System (PeOS). In collaboration with NVIDIA, Peptone developed PeOS to handle massively parallel molecular simulations. The core functionality of the platform is an automated search for non-obvious protein variants with desirable therapeutic properties and cost-effective manufacturability. To build its repository of proteins, Peptone must capture, store and analyse huge amounts of data, orchestrated and supervised by reinforcement learning algorithms. Reinforcement learning is the training of machine learning models to make a sequence of decisions. The agent learns to achieve a goal in an uncertain, potentially complex environment.
To achieve the scale of compute required to develop the PeOS, Peptone sought to use GPU-accelerated computing in the form of a NVIDIA DGX A100 supercomputer located at Verne Global's datacentre in Keflavik, Iceland, as it forms part of the NVIDIA DGX-Ready Data Centre Program and is optimised to maintain and support high density and HPC applications running on NVIDIA infrastructures. Additionally, it was important to Peptone that the datacenter is powered by 100 percent renewable energy in line with its commitment to sustainability without compromising security. Ultimately, the PeOS will handle a variety of mundane and complex tasks that are related to anomaly detection, risk of failure calculation and suggest the most plausible routes of failure resolution, including choosing the right commercial partner to generate lab-quality molecule at a pace and cost not attainable before in the Big Pharma sector.
The Scan Partnership
Peptone approached the Scan AI team, as a leader in the UK AI market, to help it find a solution to delivering significant but cost-effective GPU-accelerated compute resource. Taking advantage of its long-standing relationship with NVIDIA, Scan AI helped Peptone unlock the potential of its research by running its deep neural network models on an NVIDIA DGX A100 system. Working together with Scan, the next task was to find a datacentre facility equipped to host and support this highly specialised equipment. In addition, with privacy and security top-of-mind for Peptone’s pharmaceutical customers, there was a reluctance to place this valuable, proprietary data in the cloud. One of Scan’s datacentre partners, Verne Global, was identified as a provider that could fulfil all these criteria.
"Scan and Verne Global are the ideal partners for our hybrid supercomputing cloud approach due to its foundation in sustainability, global connectivity and reassuring ability to keep our world-leading practical research completely secure."
– Dr. Kamil Tamiola - Founder & CEO, Peptone
"Verne Global as datacentre partner, is powered by 100 percent renewable geothermal and hydroelectric energy sources, is optimised for the secure and scalable high-intensity computing required by Peptone to successfully meet the growing demands of the protein therapeutics market and accelerate the time to market of protein-based drugs."
– Dominic Ward - CEO, Verne Global
