Structure-based virtual screening software tools | Drug discovery data analysis
One of the most widely used techniques for ligand virtual screening is structure-based molecular docking to model the binding pose of a ligand in the binding site of the receptor protein followed by the prediction of binding affinity and/or free energy. In contrast to ligand-based approaches that need an initial set of bioactive compounds, the only experimental data required for structure-based docking is the 3D structure of the protein target, although homology models can be used instead.
An open source chemistry toolbox. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Permits to change a raw Protein Data Bank (PDB) structure into all-atom. Protein Preparation Wizard ensures the accuracy of all downstream modeling simulations. It aims to improve protein and ligand preparation in order to produce better virtual screening enrichments. The tool proceeds to an H-bond network optimization and geometry minimization to prepare proteins. It is able to automatically add missing hydrogen atoms and correct metal ionization states to ensure proper formal charge and force field treatment.
A fast force field generation tool able to generate, for arbitrary small organic molecule, topologies, and parameters based on the Merck molecular force field (MMFF), but in a functional form that is compatible with the CHARMM force field. SwissParam output files are formatted to be used with the CHARMM or GROMACS13 programs. After submitting the Mol2 file for a molecule on the SwissParam website, the user receives the topology and parameter files by email within minutes.
Combines major application areas in modern early drug discovery. LeadIt is an application that offers an interactive graphical user interface (GUI) which embeds both long-standing and award-winning docking. For the highly configured and advanced applications, this resource represents direct access through its command line mode with scripting facilities. It also permits the access of advanced fragment-based design tools FlexX and ReCore.
Analyzes and identifies binding sites, and predicts target druggability. SiteMap studies the druggability of proteins as measured by their ability to bind passively absorbed small molecules tightly. For helping users, this tool supplies several contents and graphical information. These data helps to modify ligand structure to enhance potency or improve physical properties in a lead-optimization context or assess virtual hits in a lead-discovery application.
Identifies shape similarity for virtual screening and lead hopping. ROCS is a virtual screening tool that can identify potentially active compounds by shape comparison, using the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. The software performs large scale 3D database searches by using a superposition method that finds the similar but non-intuitive compounds which are valuable in the drug discovery process.