Applications of FlexAID Software

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.

Our Services Based on FlexAID Software

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:

• Molecular Visualization
  Proteins and ligands are invisible to the naked eye, so visualizing results requires modeling, scientific illustration, and 3D art. Molecular visualizations provide scientific insights and can be powerful educational tools.
• Small-molecule Protein Docking
  Small molecule protein docking is an important tool for drug design and understanding molecular recognition. FlexAID allows complete ligand flexibility as well as the flexibility of the target side chain. CD ComputaBio uses the characteristics of this software to solve the problem that flexible docking requires a large amount of calculation and consumes a lot of computer time
• Docking Score
  FlexAID utilizes a soft scoring function, a scoring function based on surface complementarity that is not highly dependent on specific geometric criteria. From the ligand's 3D geometry, CD ComputaBio calculates the docking score after molecular docking. And the docking score indicates how strongly the ligand binds to the protein.

Our Capabilities

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.

Features of FlexAID Software

• Unlike other programs, FlexAID is robust against increasing structural variability.
• FlexAID achieves a sampling success rate comparable to GOLD and outperforms AutoDock Vina or FlexX for non-native complex structures in all scenarios.
• FlexAID is superior to rDock when at least one critical side chain movement is required for ligand binding. In virtual screening, FlexAID re-scoring results were comparable to those of AutoDock Vina and rDock.
• FlexAID is a welcome addition to existing small molecule protein docking methods.