Schrödinger frequently makes new scripts, structure libraries, and models from publications available. The Script Center on the Schrödinger website is a repository for utilities, automation tools, and specialized interfaces designed to work with Schrödinger software. The scripts are available free of charge to users of Schrödinger software, and can be customized for specialized applications or used out of the box without any modifications.
Below, we highlight some of the scripts that our customers find most useful.
Prime MM-GBSA interface: This graphical user interface allows researchers to easily set up, launch, and incorporate the results of Prime MM-GBSA binding energy predictions within Maestro.
Protein preparation wizard: Protein preparation is an essential prerequisite for accurate results in structure-based drug design. The protein preparation wizard automates the process of assigning appropriate hydroxyl and thiol torsions, fixing incorrectly positioned side chains, and performing a restrained minimization to eliminate unrealistic bond lengths and angles.
Glide cross-docking interface: When performing docking accuracy studies or dealing with flexible residues in a receptor active site, it is sometimes necessary to dock a ligand library against an ensemble of known or predicted receptor structures. The Glide cross-docking interface automates and simplifies the process of setting up, running, and interpreting the results of docking across multiple receptor models.
Simplified interfaces: The Schrödinger Script Center features a number of simplified application interfaces for researchers who wish to run calculations with out-of-the-box settings. The various interfaces facilitate common tasks for medicinal chemists, Glide docking calculations, and custom Jaguar batch scripts.
In addition to the tools available on the Script Center, Schrödinger also makes useful structures and structure libraries available for download. One such structure library is the CombiGlide Diverse Side-Chain Collection, a library of diverse representative functional groups commonly found in pharmaceuticals, with linkers of variable length. All reasonable ionization and tautomeric states are included. When used with CombiGlide, this collection allows exploration of an active site to identify functional groups that interact with the binding site in an energetically favorable manner.
The full collection includes approximately 1100 species, and a smaller subset of approximately 200 species is also available. Schrödinger also supplies tools for selecting subsets for use as smaller collections, and plans on significant enhancements to these selection utilities in the forthcoming 2007 software release. The collection is available here.