CLC Drug Discovery Workbench
A virtual lab bench developed specifically for bench chemists and biochemists, to inspire and facilitate drug design improvements.
A virtual lab bench for chemists
CLC Drug Discovery Workbench is your new virtual lab bench. It gives you access to atomic level insights in protein-ligand interaction, and allows new ideas for improved binders to be quickly tested and visualized.
The workbench empowers bench chemists as well as computational chemists to analyze and visualize protein targets and ligands binding to them. The intuitive and powerful interface is designed to communicate with all chemists, with no assumptions about their level of theoretical training. Medicinal chemists can visualize and model molecule interactions to work with ideas in a frictionless manner, thus fueling innovation.
CLC Drug Discovery Workbench is part of the CLC bio Enterprise Platform with support for workflows, client-server setup, and command-line tools. Furthermore, like all other workbenches from CLC bio, the Drug Discovery Workbench runs on Mac OS X, Windows, and Linux platforms.Download CLC Drug Discovery Workbench product sheet
Quick Guide - Exploring protein-ligand Binding
Quick Guide - Virtual Screening
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For a diverse set of 85 high resolution protein-ligand complexes* relevant to the pharmaceutical or agrochemical industry, it is tested how many of the complexes can be reproduced in molecular docking with a ligand binding mode with RMSD of less than 2 Å.
CLC Drug Discovery Workbench is based on CLC bio’s market-leading platform for data analysis, and comes with CLC bio sequence analysis tools integrated:
Molecule Structure Visualization
- Molecule 3D structure import: Mol2, SDF, PDB
- Search for PDB structures at NCBI
- Molecule 3D structure export: Mol2
- Quick-style options including ball-n-sticks and molecular surfaces
- Custom visualization applied to selected atoms
- Molecule tables with 2D depiction of molecules
- Molecule 3D structure generation from SMILES or 2D representation*
- Automatic assignment of missing atom and bond properties
- Automatic docking target setup
- Chemical consistency checker
Structure Based Drug Discovery
- Manually adjust atom and bond properties
- Binding pocket finder
- Easy, graphical docking target setup
- Fast track molecular docking
- Virtual screening
- Size of molecule libraries not limited by memory
- Ligand binding inspection
Sequence analysis tools
- Search for sequences at UniProt
- Phylogenetic trees
- Prediction of transmembrane helices
- Motif search
- Pfam domain search
* The freely available program Balloon is used as an engine for generating 3D coordinates for the molecule on import
Structure Based Drug Discovery Features
Ligands can be docked with one click in the graphical user interface, or through a wizard, allowing customization of sampling and output. Huge molecule libraries are handled in Molecule Tables for use in virtual screenings. Potential ligand binding sites can be located with the binding pocket finder. The binding modes of ligands, being co-crystallized or resulting from docking, can be inspected in detail using automatically generated visualizations of the interactions between ligand and docking target.