Resources made (coming soon) publicly available include software, databases, and parameter sets for computational models. The York Lab are developers of the CHARMM and AMBER suite of molecular modeling software suites. Many of the new innovations coming from the lab are part of our own software libraries and tool sets that can be used either stand-alone or interfaced with molecular simulation software. Our main database of quantum chemical calculations for RNA catalysis (QCRNA) is also available along with search and query tools.
The York Lab develops a variety of software for multiscale modeling, including linear-scaling methods for electrostatic interactions, solvation and electronic structure. These methods are integrated into molecular simulation software, including CHARMM and AMBER, so that it can be applied to study complex biological problems. In addition, the York Lab develops methods for analyzing simulation data, including variational methods to generate free energy profiles, methods to determine NMR parameters, and compute kinetic isotope effects.
The DFT Database for RNA Catalysis is a large collection of high-level density-functional electronic structure calculations of molecules, complexes and reactions relevent to RNA Catalysis. This is part of a 5-year project funded by the NIH to study the molecular mechanisms of RNA enzymes, or ribozymes. A detailed understanding of RNA catalysis is fundamental to biology, and has important implications toward the design of new medical therapies that target genetic disorders as well as the development of new biotechnology. The DFT Database for RNA Catalysis can be used to derive information about molecular structure, compelxes and reactions.