Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein

A discard-and-restart MD algorithm for the sampling of protein intermediate states

We introduce a discard-and-restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein intermediate states. It aids computational structure-based drug discovery by reducing the simulation times to compute a "quick sketch" of folding pathways by up to 2000×. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective variable loss, which can be defined in a flexible fashion, locally or globally. Using the loss, if the trajectory proceeds toward the target, the MD simulation continues. Otherwise, it is discarded, and a new MD simulation is restarted, with new initial velocities randomly drawn from a Maxwell-Boltzmann distribution. The discard-and-restart algorithm demonstrates efficacy and atomistic accuracy in capturing the folding pathways in several contexts: 1) fast-folding small protein domains, 2) the folding intermediate of the prion protein PrP, and 3) the spontaneous partial unfolding of α-tubulin, a crucial event for microtubule severing. During each iteration of the algorithm, we can perform AI-based analysis of the transitory conformations to find potential binding pockets, which could represent druggable sites. Overall, our algorithm enables systematic and computationally efficient exploration of conformational landscapes, enhancing the design of ligands targeting dynamic protein states.

RISMiCal: A software package to perform fast RISM/3D-RISM calculations

Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.