Molegro Product Datasheet Molegro Virtual Docker High accuracy molecular docking Molegro Virtual Docker is an integrated platform for predicting protein - ligand interactions. It handles all aspects of the process, from preparing the molecules to determining the potential binding site of the target protein, and predicting the binding mode of the ligand. Molegro Virtual Docker offers high-quality docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity. Molegro Virtual Docker Overview High docking accuracy: the docking engine has been proven to correctly identify binding modes with high accuracy (see next page). Versatile features including induced fit docking (sidechain flexibility), ligand- based screening based on structural similarity, flexible alignment of small molecules, and regression model building using neural nets or MLR. Advanced visualization and analysis tools are provided to examine ligand- receptor interactions and fine-tune found docking solutions. Grid computing: distribute the docking simulations on multiple computers using Molegro Virtual Grid. Cross-platform: Windows, Mac, and Linux. The main user interface of Molegro Virtual Docker. Basic Features Import and export of industry standard file formats (PDB, Mol2, SDF). Automated preparation of input structures (assign hydrogens, charges, bond orders, hybridization, protonation templates). Visualization styles (wireframe, ball-and- stick, CPK, stick, cartoon, and surfaces). Automatic prediction of potential binding sites (active site finding). Built-in raytracer for making high- quality images. Multiple docking scoring functions. Docking search algorithms based on state-of-the-art optimization algorithms. Console command interface to allow for advanced user interaction. GUI wizards and on-line help. Benchmark Results Docking ProgramAccuracy Molegro Virtual Docker87,0% Glide81,8% GOLD178.2% Surflex75.3% FlexX257.9% Table 1: Accuracy of selected docking programs on 77 complexes. See MolDock: A New Technique for High-Accuracy Molecular Docking: Ren Thomsen and Mikael H. Christensen (J. Med. Chem., 2006, 49(11), pp 3315 3321) for more details. 1 Based on 55 out of the 77 complexes 2 Based on 76 out of the 77 complexes Advanced Features Visual inspection of docked conformations displaying relevant interactions. Repair, mutate, or minimize sidechains before docking. Docking with sidechain flexibility taking induced fit interactions into account. Molecular descriptor calculation, including our unique CFDM topological descriptors. Reranking score (rerank docked solutions to increase docking accuracy). Docking using precalculated energy grids to speed up calculations. Data Analyzer for creating regression models (using neural networks or MLR) and visualizing data. Displaceable water model for docking with explicit water molecules. Similarity Docking for flexible ligand alignment and focused docking/screening using templates (pharmacophores). User-defined constraints to increase docking performance. Advanced Features (continued) Biomolecule generator. Structural Protein Alignment. Pose Modifier for manually modifying poses. RMSD measure taking automorphisms into account. Ligand Energy Inspector. Spherical cropping tool. Sequence viewer. Support for scripting of the docking engine (Python wrapper included). Supported PlatformsEvaluation Copies Windows 7, Vista, XP, and 2003. Mac OS X 10.4 or later (Intel & PowerPC). Linux: Most major distributions including Fedora Core, Red Hat, and Ubuntu. Both 32 and 64 bit versions are available. To request a 30 day trial version visit Additional Information info About Molegro Molegro develops bioinformatics software for drug discovery and data mining. We focus on combining state-of-the-art algorithms with an intuitive graphical user interface experience. Through collaboration with both academia and industry we ensure our products are continuously evolving. Molegro C. F. Moellers Alle 8, Building 1110 DK-8000 Aarhus C Denmark Phone: (+45) 89 42 31 65 Fax: (+45) 89 42 30 77