Theoretical and Computational Chemistry




Ligand-induced conformational changes form the underpinnings of most essential biomolecular processes, however they are often neglected in screening and design applications, due to the high computational cost. We propose a method called “Flexible Topology”, where a ligand is comprised of a set of shapeshifting “ghost” atoms, whose atomic identities and connectivity can dynamically change over the course of a simulation. Ghost atoms are guided toward their target positions using a translation-, rotation-, and index-invariant restraint potential. When implemented with a large set possible targets, this can simulate trajectories in a coupled chemical-conformational space that allows solutions to molecular design problems to simply emerge over the course of a trajectory. It also provides a mechanism for observing ligand-induced conformational change, by allowing for the surrounding environment and the ghost atoms to respond to each other during the design process. This builds on a substantial history of alchemy in the field of molecular dynamics simulation, including the Lambda dynamics method developed by Brooks and coworkers [X. Kong and C.L. Brooks III, J. Chem. Phys. 105, 2414 (1996)], but takes it to an extreme by associating a set of four dynamical variables with each shapeshifting atom that control not only its presence but its atomic identity. Here we outline the theoretical details of this method, its implementation using the OpenMM simulation package, and some preliminary studies of ghost particle assembly simulations. We show that while Flexible Topology is able to consistently assemble molecules up to 50 atoms in size, modifications are needed before it can reliably predict bound poses in heterogeneous environments.


Thumbnail image of flex_top_arxiv.pdf

Supplementary weblinks

MLForce github repository
A repository containing files, examples and installation instructions for MLForce, a package that allows PyTorch models to be used to define external forces in OpenMM simulations.
FlexibleTopology github repository
A repository containing files, examples and installation instructions for FlexibleTopology, a package that helps construct objects such as CustomIntegrators and custom forces that are needed to conduct flexible topology simulations in OpenMM.