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In silico drug design (CADD)

In silico drug design (CADD)In silico drug design (CADD)In silico drug design (CADD)In silico drug design (CADD)In silico drug design (CADD)

We are proud to offer our best expertise and 1st-class services to your organization

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ChemDiv’s CADD team can help accelerate the early stages of your drug discovery project. Experienced scientists with background in molecular modeling, data mining, and cheminformatics work closely with medicinal chemists and biologists.

We provide a number of sophisticated computational services as a part of larger integrated projects or as stand-alone in silico services:

  • Structure Based Drug Design – Docking, Molecular Dynamic
  • Ligand Based Drug Design- Similarity, Pharmacophore models
  • Virtual Screening – HTS support, focused libraries design
  • Hit2lead optimization – ADME optimization, scaffold hopping
  • and other


  • Molsoft ICM Pro – Molecular docking, ligand binding sites identification, etc.
  • Cresset Flare and Forge – Structure and ligand-based design
  • Autodock4, Autodock Vina (Scripps) – Molecular docking
  • ChemoSoft (ChemDiv) – 2D similarity, combinatorial chemistry
  • Knime – Workflows for ETL and data preparation tasks
  • Rdkit (Python), Open Babel – Custom cheminformatics solutions
  • Python, DataWarrior – Chemical space visualization
  • Gromacs – Molecular dynamics simulations

Why work with us?

  • Wide experience in in silico drug design
  • We have access to the large diverse (1.6M compounds) library of small molecules ready for biological trials
  • World-class software and hardware equipment
  • Solid scientific expertise in fields of medicinal chemistry and cheminformatics

Virtual screening

Screening library design and subset selection.

Virtual Screening - Screening libraries, chemical libraries and screening compounds

ChemDiv Inc. is a recognized leader in this field. Using our 1.6 million collection of stock compounds, we can develop a focused library to meet your needs. Our small molecule library is growing by ~ 100 thousand compounds annually. According to our estimates, the chemical space of the synthesizable compounds exceeds 20M. To order synthesis services, visit our Custom Chemistry page.

Construction of a focused libraries using ligand and structure-based methods to reduce costs of HTS.

  • Physicochemical properties prediction
  • Similarity search
  • 3D pharmacophore models
  • Flexible docking
  • Analysis of the HTS data to select the most perspective compounds for further optimization

Contact us to learn more: chemdiv@chemdiv.com

Ligand based drug design

Ligand based approach is one of the fastest and widely used methods to identify and optimize new hits.

Ligand Based Drug Design
  • Chemical space visualization, clusterization based on scaffolds and similarity metrics
  • Predictive QSAR models
  • Pharmocophore models, 3D alignment
  • Conformational analysis
  • Combinatorial chemistry and in silico generation of new structures
  • Scaffold hopping and fragment replacement
  • Synthesability assessment of generated structures

Contact us to learn more: chemdiv@chemdiv.com

Structure based drug design

If reliable structural information about target and/or mode of ligand binding is available, structure based methods could accompany ligand based approaches to help in design and optimization of novel compounds.

Structure Based Drug Design
  • Protein structure refinement, loop modeling
  • Binding site identification
  • Homology modeling
  • Flexible docking – induced fit, etc.
  • Docking based QSAR models (Docking to Protein Pocket Classification/Regression (dpc) models as implemented in Molsoft package)
  • Molecular dynamics studies for additional analysis of binding mode

Contact us to learn more: chemdiv@chemdiv.com

Hit2lead optimization

Hit to lead optimization extensively uses both structure-based and ligand-based methods.

Hit2lead optimization

We provide:

  • Rapid analysis of hits obtained by high throughput screening (HTS)
  • Chemical space visualization of obtained hits
  • In silico profiling:
       ○ ADMET optimization
       ○ Scaffold hopping

Contact us to learn more: chemdiv@chemdiv.com

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