FlexAID is an open-source molecular docking software developed by Najmanovich Research Group. FlexAID can use small molecules and peptides as ligands, and proteins and nucleic acids as docking targets. FlexAID supports full ligand flexibility as well as targeted side-chain flexibility. It does use a soft scoring function based on the complementarity of the two surfaces (ligand and target). FlexAID utilizes soft scoring functions that are not highly dependent on specific geometric criteria, based on surface complementarity. The energy parameter of the scoring function is derived from the classification of a large dataset of native and near-native (less than 2Å RMSD) conformations of nearly 1500 complexes from the PDBbind database. These are countered by successive rounds of Monte Carlo optimizations with RMSDs above 2 Å on increasingly lower energy decoys. The FlexAID source code is available on Najmanovich Research Group's GitHub page.
FlexAID can achieve better accuracy than existing widely used or state-of-the-art methods in predicting the structure of ligand-protein complexes. FlexAID and its GUI integrated with PyMOL are free, easy to use, and available for Windows, Linux, and Mac OS. On the FlexAID software platform, CD ComputaBio can provide the listed services:
We have the expertise and experience to extract, structure, process, and transform unstructured data into high-quality analytical-grade structured datasets. We can provide customers with technical guidance and software consultation on the FlexAID technology platform. We detect surface cavities in macromolecules, refine them, calculate volumes and use them individually or in combination as target binding sites for docking simulations with FlexAID.