Once again, CCPBioSim2025 delivered an engaging conference showcasing the frontiers of biomolecular simulation, and OpenBioSim was proud to sponsor the event. The scientific meeting took place at the University of Southampton from July 14–16. Many thanks to the organising committee for putting together such a successful event: Jonathan Essex, William Poole, Aditi Borkar, Agnieszka Bronowska, Daniel Cole, Warispreet Singh, Sofia Oliveira, James Gebbie-Rayet, and Shivani Harshe.

OpenBioSim’s projects, Sire and BioSimSpace, were featured in several talks and poster presentations throughout the meeting:

  • Frederick Powell (Heriot-Watt University) gave a talk titled “In Search of Enzyme Activation: A Markov State Model Approach to Allosteric Drug Discovery.” Frederick’s work leverages the AMMo software, built on top of BioSimSpace. This work was recently published in Chemical Science.
  • Joao Morado (University of Edinburgh) gave a talk on “Enhancing Electrostatic Embedding for ML/MM Free Energy Calculations: Strategies for Accurate and Transferable Models.” Joao used Sire to perform hydration free energy calculations with various hybrid machine learning/molecular mechanics methodologies. A preprint describing this work has recently been posted.
  • Jasmin Guven (University of Edinburgh) presented a talk titled “Potential β-lactamase Inhibitors Under the Alchemical Microscope,” featuring the use of BioSimSpace to benchmark the binding affinities of different families of β-lactamase enzymes. This work was also featured in an earlier blog post.
  • Roy (Haolin) Du (University of Edinburgh) presented a poster on “Scaling Absolute Binding Free Energy Calculations for Virtual Screening.” This work furthers the automation of the A3FE software, built on top of Sire and BioSimSpace, to enable processing of large datasets of small-molecule binders using alchemical absolute binding free energy calculation methods.
  • Chenfeng Zhang (University of Edinburgh) presented a poster titled “Which Binder Can Master the Master Kinase PDK1?” This work also utilises the AMMo software to computationally profile allosteric modulators.
  • Matthew Burman (OpenBioSim) presented a poster on recent developments in “SOMD2: A Modular and Extensible Open-Source Engine for GPU-Accelerated Free Energy Calculations.”
  • Finally, Ziwei Pang (University of Oxford) won the OpenBioSim-sponsored poster prize for his work on “Leveraging Multiple Short MD Simulations for Screening PepT2 Transporter Substrates.”

Looking forward to CCPBioSim 2026 !

 

Written by Julien Michel