CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein.

The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE challenge in which 23 computational teams each selected up to 100 commercially available compounds that they predicted would bind to the WDR domain of the Parkinson's disease target LRRK2, a domain with no known ligand and only an apo structure in the PDB. The lack of known binding data and presumably low druggability of the target is a challenge to computational hit finding methods.

TrIP─Transformer Interatomic Potential Predicts Realistic Energy Surface Using Physical Bias.

Accurate interatomic energies and forces enable high-quality molecular dynamics simulations, torsion scans, potential energy surface mappings, and geometry optimizations. Machine learning algorithms have enabled rapid estimates of the energies and forces with high accuracy. Further development of machine learning algorithms holds promise for producing universal potentials that support many different atomic species.

Ozone exposure-response relationships parametrized for sixteen tree species with varying sensitivity in the United States.

It is well known that exposure to ambient O can decrease growth in many tree species in the United States (US). Our study reports experimental data from outdoor open-top chamber (OTC) studies that quantify total biomass response changes for seedlings of 16 species native to western and eastern North America, which were exposed to several levels of elevated O for one or more years. The primary objective of this study is to establish a reference set of parameters for these seedling exposure-response relationships using a 3-month (92 day) 12-hr W126 O metric used by US Environmental Protection Agency and other agencies to assess risk to trees from O exposure.

Physiological responses of Douglas-fir to climate and forest disturbances as detected by cellulosic carbon and oxygen isotope ratios.

Swiss needle cast (SNC), caused by a fungal pathogen, Nothophaeocryptopus gaeumannii, is a major forest disease of Douglas-fir (Pseudotsuga menziesii) stands of the Pacific Northwest (PNW). There is mounting concern that the current SNC epidemic occurring in Oregon and Washington will continue to increase in severity, frequency and spatial extent with future warming. Nothophaeocryptopus gaeumannii occurs wherever its host is found, but very little is known about the history and spatial distribution of SNC and its effects on growth and physiological processes of mature and old-growth forests within the Douglas-fir region of the PNW.