Highlights from the CCPBioSim conference, Newcastle, July 1-3, 2024

CCPBioSim delivered a fantastic 2.5-day conference in Newcastle on July 1-3, 2024, thanks to the local organising committee: Daniel Cole, Natalie Tatum, Agnieszka Bronowska, and Katie Sawyer. There were about 90 in-person delegates and 30-40 online delegates.

Throughout the meeting, multiple talks and posters showcased the use of OpenBioSim’s software projects to support a broad range of scientific studies.

  • Antonia Mey presented a talk highlighting the use of BioSimSpace for accurate FEP modeling of beta-lactamase inhibitors.
  • Finlay Clark gave a talk on the A3FE methodology for automated adaptive absolute binding free energy calculations using BioSimSpace and Sire. More details area available in a preprint, and on Github.
  • Salome Llabres discussed the use of ABFE calculations with Sire, in combination with conformational free energy landscape calculations, NMR, and ITC experiments, to elucidate the mechanism of folding of an intrinsically disordered protein region in the protein MDM2 upon binding of a small molecule (More details in this paper and preprint).
  • Matthew Burman presented a poster on the software SOMD2, a general-purpose open-source alchemical free energy calculation engine based on the Sire and OpenMM libraries currently under development at OpenBioSim.
  • Audrius Kalpokas showcased in a poster the use of BioSimSpace and GROMACS to investigate the effects of mutations in disordered protein regions on ligand binding via protein FEP protocols.
  • Chenfeng Zhang presented a poster on mechanistic studies of allosteric modulation of the protein kinase PDK1 via the AMMo software, an open-source project built on top of BioSimSpace.
  • Joao Morado described in a poster hydration free energy calculations using machine learning potentials and ML/MM electrostatic embedding an integration of the EMLE engine with Sire.
  • Finally, Diana Veselu won a poster prize sponsored by OpenBioSim for her work on “Investigating Targeted Therapies for Cystic Fibrosis through D-NEMD Simulations of the CFTR Protein.”

Many thanks to all the delegates for making CCPBioSim 2024 such a resounding success.

 

 

Antonia Mey CCPBIoSim2024
Finlay Clark CCPBioSim2024

Salome Llabres CCPBioSim2024

OpenBioSim poster prize CCPBioSim2024

 

 

Written by Julien Michel