Ross Read

© 2016 Elsevier Ltd All rights reserved.Crystallographic studies of ligands bound to biological macromolecules represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

I argue that the type of progress exhibited by philosophy is not that exhibited by science, but rather is akin to the kind of progress exhibited be someone becoming ‘older and wiser’. However, as actually-existing philosophy has gotten older, it has not always gotten wiser. As an illustration, I consider Rawls's conception of justification. I argue that Rawls's notion of what it is to have a philosophical justification exhibits no progress at all from Euthyphro's. In fact, drawing on a remark of Wittgenstein's, I suggest that Rawls's conception is inferior to the situation as depicted in Plato's famous dialogue – because at least in the case of Plato's Euthyphro, there is no illusion of justification.