Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently.

Conformational changes underpin function and encode complex biomolecular mechanisms. Gaining atomic-level detail of how such changes occur has the potential to reveal these mechanisms and is of critical importance in identifying drug targets, facilitating rational drug design, and enabling bioengineering applications. While the past two decades have brought Markov state model techniques to the point where practitioners can regularly use them to glimpse the long-time dynamics of slow conformations in complex systems, many systems are still beyond their reach. In this Perspective, we discuss how including memory (i.e., non-Markovian effects) can reduce the computational cost to predict the long-time dynamics in these complex systems by orders of magnitude and with greater accuracy and resolution than state-of-the-art Markov state models. We illustrate how memory lies at the heart of successful and promising techniques, ranging from the Fokker-Planck and generalized Langevin equations to deep-learning recurrent neural networks and generalized master equations. We delineate how these techniques work, identify insights that they can offer in biomolecular systems, and discuss their advantages and disadvantages in practical settings. We show how generalized master equations can enable the investigation of, for example, the gate-opening process in RNA polymerase II and demonstrate how our recent advances tame the deleterious influence of statistical underconvergence of the molecular dynamics simulations used to parameterize these techniques. This represents a significant leap forward that will enable our memory-based techniques to interrogate systems that are currently beyond the reach of even the best Markov state models. We conclude by discussing some current challenges and future prospects for how exploiting memory will open the door to many exciting opportunities.

Building insightful, memory-enriched models to capture long-time biochemical processes from short-time simulations.

The ability to predict and understand complex molecular motions occurring over diverse timescales ranging from picoseconds to seconds and even hours in biological systems remains one of the largest challenges to chemical theory. Markov state models (MSMs), which provide a memoryless description of the transitions between different states of a biochemical system, have provided numerous important physically transparent insights into biological function. However, constructing these models often necessitates performing extremely long molecular simulations to converge the rates. Here, we show that by incorporating memory via the time-convolutionless generalized master equation (TCL-GME) one can build a theoretically transparent and physically intuitive memory-enriched model of biochemical processes with up to a three order of magnitude reduction in the simulation data required while also providing a higher temporal resolution. We derive the conditions under which the TCL-GME provides a more efficient means to capture slow dynamics than MSMs and rigorously prove when the two provide equally valid and efficient descriptions of the slow configurational dynamics. We further introduce a simple averaging procedure that enables our TCL-GME approach to quickly converge and accurately predict long-time dynamics even when parameterized with noisy reference data arising from short trajectories. We illustrate the advantages of the TCL-GME using alanine dipeptide, the human argonaute complex, and FiP35 WW domain.

Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.

Binding MOAD is a database of protein-ligand complexes and their affinities with many structured relationships across the dataset. The project has been in development for over 20 years, but now, the time has come to bring it to a close. Currently, the database contains 41,409 structures with affinity coverage for 15,223 (37%) complexes. The website BindingMOAD.org provides numerous tools for polypharmacology exploration. Current relationships include links for structures with sequence similarity, 2D ligand similarity, and binding-site similarity. In this last update, we have added 3D ligand similarity using ROCS to identify ligands which may not necessarily be similar in two dimensions but can occupy the same three-dimensional space. For the 20,387 different ligands present in the database, a total of 1,320,511 3D-shape matches between the ligands were added. Examples of the utility of 3D-shape matching in polypharmacology are presented. Finally, plans for future access to the project data are outlined.