Molecular Docking

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, and how the ligands inhibit the target, which is invaluable in lead optimization. Open access to the scientific literature means the removal of barriers (including price barriers) from accessing scholarly work. There are two parallel “roads” towards open access: Open Access articles and self-archiving. Open Access articles are immediately, freely available on their Web site, a model mostly funded by charges paid by the author (usually through a research grant). The alternative for a researcher is “self-archiving” (i.e., to publish in a traditional journal, where only subscribers have immediate access, but to make the article available on their personal and/or institutional Web sites (including so-called repositories or archives)), which is a practice allowed by many scholarly journals. Open Access raises practical and policy questions for scholars, publishers, funders, and policymakers alike, including what the return on investment is when paying an article processing fee to publish in an Open Access articles, or whether investments into institutional repositories should be made and whether self-archiving should be made mandatory, as contemplated by some funders.