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 a novel optimization

technique combined with a user interface experience focusing on usability and
productivity.

The main user interface of Molegro Virtual Docker.

Molegro Virtual Docker at a Glance

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.
Easy-to-use interface: the built-in
wizards enable the user to easily setup
and perform docking runs. Advanced
visualization and analysis tools are
provided to examine ligand-receptor
interactions and fine-tune found
docking solutions.
Cross-platform: supported on Linux,
Windows, and Mac, allowing easy
interoperability between platforms.
 Basic Features
Import and export of industry standard
file formats (PDB, Mol2, SDF)
Automated preparation of input structures
(assign hydrogens, charges, bond orders,
hybridization)
Visualization styles (wireframe, ball-and-
stick, CPK, stick, cartoon, and surfaces)
Automatic prediction of potential binding
sites (active site finding)
Flexible 3D-label system
Docking scoring function (extended
PLP score taking hydrogen bonding
directionality into account)
Docking search algorithm based on
state-of-the-art genetic algorithms
Console command interface to allow
for advanced user interaction
GUI wizards and on-line help

Benchmark Results
Docking Program Accuracy
Molegro Virtual Docker 87.0%
Glide 81.8%
GOLD1 78.2%
Surflex 75.3%
FlexX2 57.9%
Table 1: Accuracy of selected docking programs on 77 complexes. See 'MolDock:
A New Technique for High-Accuracy Molecular Docking': René 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
Sidechain minimization tool for optimizing
receptor conformation before docking
Docking with sidechain flexibility taking
induced fit interactions into account
Data Analyzer for creating regression
models (using neural networks or MLR)
and visualizing data
The user interface can be customized and
extended via the built-in macro language
Ability to only report diverse
conformations based on a clustering
measure
Reranking score (rerank docked solutions
to increase docking accuracy)
Docking using precalculated energy grids
to speed up calculations
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 Ligand Energy Inspector
Structural Protein Alignment Support for batch jobs – distribute the
Spherical cropping tool docking simulations on multiple
computers
Sequence viewer
Support for scripting of the docking
RMSD measure taking automorphisms
engine (Python wrapper included)
into account

Supported Platforms Evaluation Copies

Windows Vista, XP, 2003, and 2000 To request a 30 day trial version visit
Mac OS X 10.4 or later (Intel and PPC) http://www.molegro.com/products.php
Linux: Most major distributions including
Fedora Core, Red Hat, and Ubuntu. Both Additional Information
32 and 64 bit versions are available. www.molegro.com
info@molegro.com

About Molegro

The name 'Molegro' is a combination of the words Molegro ApS

'Molecule' and 'Allegro' (Italian for rapid). The core Hoegh-Guldbergs Gade 10, Bldg. 1090
of our business is high-performance drug discovery DK-8000 Aarhus C - Denmark

solutions leading to a faster drug-development Phone: (+45) 89 42 31 65

Fax: (+45) 89 42 30 77
process.