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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.Product sheetQuick Guide - Molecule visualizationsQuick Guide - Fast Track DockingQuick Guide - Hit to LeadQuick Guide - Virtual ScreeningQuick Guide - Protein Insights



Accuracy Benchmark

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 - Accuracy Benchmark


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
  • Direct download of PDB structures from NCBI
  • Quick-style options including ball-n-sticks and molecular surfaces
  • Custom visualization applied to selected atoms
  • Save molecule visualizations on data
  • Molecule tables with 2D depiction of molecules

Chemical Awareness

  • Generate molecule 3D structure from SMILES or 2D representation*
  • Automatic assignment of missing atom and bond properties
  • Automatic binding site setup
  • Chemical consistency checker
  • Lipinski’s rule of five check

Structure Based Drug Discovery

  • Binding pocket finder
  • Easy, graphical protein target setup
  • Fast track molecular docking
  • Optimize ligand interactions in binding site
  • Virtual screening
  • Repair or change amino acids
  • Calculate molecular properties
  • Protein structure and binding site alignment

Sequence Analysis and Modeling

  • Search for sequences at UniProt
  • Create protein structure homology model
  • Sequence alignment and phylogenetic trees
  • Motif and Pfam domain search
* The freely available program Balloon is used as an engine for generating 3D coordinates for the molecule on import


The looks

Latest improvements

We frequently release updates and improvements such as bug fixes, new features or plugins. To get a complete overview, please visit our latest improvements page.