Machine Learning Guided AQFEP: A Fast and Efficient Absolute Free Energy Perturbation Solution for Virtual Screening.

Structure-based methods in drug discovery have become an integral part of the modern drug discovery process. The power of virtual screening lies in its ability to rapidly and cost-effectively explore enormous chemical spaces to select promising ligands for further experimental investigation. Relative free energy perturbation (RFEP) and similar methods are the gold standard for binding affinity prediction in drug discovery hit-to-lead and lead optimization phases, but have high computational cost and the requirement of a structural analog with a known activity. Without a reference molecule requirement, absolute FEP (AFEP) has, in theory, better accuracy for hit ID, but in practice, the slow throughput is not compatible with VS, where fast docking and unreliable scoring functions are still the standard. Here, we present an integrated workflow to virtually screen large and diverse chemical libraries efficiently, combining active learning with a physics-based scoring function based on a fast absolute free energy perturbation method. We validated the performance of the approach in the ranking of structurally related ligands, virtual screening hit rate enrichment, and active learning chemical space exploration; disclosing the largest reported collection of free energy simulations to date.

Narratives bridge the divide between distant events in episodic memory.

Many studies suggest that information about past experience, or episodic memory, is divided into discrete units called "events." Yet we can often remember experiences that span multiple events. Events that occur in close succession might simply be linked because of their proximity to one another, but we can also build links between events that occur farther apart in time. Intuitively, some kind of organizing principle should enable temporally distant events to become bridged in memory. We tested the hypothesis that episodic memory exhibits a narrative-level organization, enabling temporally distant events to be better remembered if they form a coherent narrative. Furthermore, we tested whether post-encoding memory consolidation is necessary to integrate temporally distant events. In three experiments, participants learned and subsequently recalled events from fictional stories, in which pairs of temporally distant events involving side characters ("sideplots") either formed one coherent narrative or two unrelated narratives. Across participants, we varied whether recall was assessed immediately after learning, or after a delay: 24 hours, 12 hours between morning and evening ("wake"), or 12 hours between evening and morning ("sleep"). Participants recalled more information about coherent than unrelated narrative events, in most delay conditions, including immediate recall and wake conditions, suggesting that post-encoding consolidation was not necessary to integrate temporally distant events into a larger narrative. Furthermore, post hoc modeling across experiments suggested that narrative coherence facilitated recall over and above any effects of sentence-level semantic similarity. This reliable memory benefit for coherent narrative events supports theoretical accounts which propose that narratives provide a high-level architecture for episodic memory.

The hippocampus constructs narrative memories across distant events.

Life's events are scattered throughout time, yet we often recall different events in the context of an integrated narrative. Prior research suggests that the hippocampus, which supports memory for past events, can support the integration of overlapping associations or separate events in memory. However, the conditions that lead to hippocampus-dependent memory integration are unclear. We used functional brain imaging to test whether the opportunity to form a larger narrative (narrative coherence) drives hippocampal memory integration. During encoding of fictional stories, patterns of hippocampal activity, including activity at boundaries between events, were more similar between distant events that formed one coherent narrative, compared with overlapping events taken from unrelated narratives. One day later, the hippocampus preferentially supported detailed recall of coherent narrative events, through reinstatement of hippocampal activity patterns from encoding. These findings demonstrate a key function of the hippocampus: the integration of events into a narrative structure for memory.