Applications of LeDock Software

LeDock is a cross-platform (Win, Linux, Mac OS) molecular docking software developed by Dr. Zhao Hongtao from the University of Zurich, which is designed for flexible docking of small molecules to proteins. It has strong advantages in speed and accuracy. It achieves greater than 90% conformational prediction accuracy on the Astex diversity ensemble.The preparation of the LeDock receptor is relatively simple, as long as the lepro program can be used to complete, including hydrogenation (pH7.0), charging (CHARMM/m charge), the residues and atoms of the receptor are in the form of CHARMM, and the extra Residue conformations will be removed, leaving only the first conformation. The preparation of ligand small molecules is relatively simple, only need to provide mol2 file. LeDock uses simulated annealing-genetic algorithm crossover algorithm for conformational search, and docking scoring covers van der Waals interaction, electrostatic interaction, hydrogen bond contribution, as well as intermolecular and intramolecular ligands.

Our Services Based on LeDock Software

On the LeDock software platform, CD ComputaBio can provide customers with high-quality computational biology services.

• Molecular Docking
  We perform protein-ligand docking to detect and measure binding interactions between targets and their ligands, supporting drug lead identification by reliably predicting the behavior of protein molecules.
• Virtual Screening
  On the LeDock software platform, we are able to identify small molecule starting points for numerous drug discovery programs on behalf of our partners against a variety of biological disease targets. In some cases, it eventually enables projects to move into drug development.
• Library Design
  Maximize your investment in compound screening with a custom compound library design. Using our extensive compound libraries, our team of biologists and chemists use LeDock software like virtual screening and modeling to design a screening set tailored to your requirements and budget.
• Big-Data Guided Optimization
  Our scientists power your compound optimization to beat the competition with LeDock software and analytical solutions
• Fragment-Based Drug Design
  Focusing on biologically active core fragments, our scientists can generate specialized fragment libraries for the increasingly popular fragment-based drug design (FBDD) and ultimately high-throughput screening (HTS) libraries.
• Hit Identification
  Hit identification typically begins with screening large compound libraries. Our scientists have achieved 10% to 40% validation hit rates for a variety of drug targets through an innovative approach to virtual screening.
• Lead Optimization
  Lead optimization is a complex iterative process that alters the chemical structures of confirmed hits to identify improved drug leads with the goal of developing into preclinical drug candidates.

Our Capabilities

Computer-aided drug design (CADD) brings innovations to drug discovery, from hit identification to lead optimization. Our scientists enable fragment-based virtual screening cascades based on unique fragmentation protocols that allow efficient navigation of a vast chemical space.

Features of LeDock Software

LeDock is designed to quickly and accurately dock small molecules into proteins flexibly. It achieves greater than 90% pose prediction accuracy on the Astex diversity set and takes about 3 seconds per run for drug-like molecules. It uses the SYBYL Mol2 format directly as input for small molecules. The graphical version of the Windows operating system greatly simplifies the many complex docking procedures commonly used by pharmacists.

• Fragments with high chemical richness
• Fragmentation frequency statistics
• Unique core segment jumps
• Basic cheminformatics analysis
• User friendly and extremely fast
• High attitude prediction accuracy
• User-friendly virtual screening and hit elaboration
• Very fast