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Molecular Docking & Drug Discovery

Structure-based screening, interaction analysis and network pharmacology as a starting point for experiments.
3D structure of the VEGFR2 kinase domain bound to sorafenib (PDB 4ASD).
RCSB PDB 4ASD · CC BY 4.0

Overview

Computational methods are a fast, inexpensive way to generate hypotheses: which compounds might bind a target, which residues are involved, and which pathways a compound set could affect. Their value depends on validation steps and on being honest about uncertainty.

Questions we can help you answer

  • Is docking appropriate for my question?
  • Which protein structure should I use?
  • How do I validate a docking protocol?
  • How should network-pharmacology results be filtered and reported?

Methods we advise on

  • Receptor and ligand preparation
  • Re-docking validation
  • Interaction analysis
  • Protein–protein interaction networks
  • GO/KEGG enrichment
  • MD planning

Please note

  • Docking scores are not binding affinities, and in silico results are not evidence of efficacy or safety.

From mechanism to structure

See the science

A signalling pathway explained step by step, and the real experimental structure of a drug bound to its target.

A growth factor binds the extracellular domain of each receptor. Ligand-bound receptors pair up (dimerise) in the membrane. The two kinase domains phosphorylate tyrosines on each other (trans-autophosphorylation). Phosphotyrosines recruit adaptor proteins (Grb2·SOS), which activate RAS. RAS → RAF → MEK → ERK relays the signal to the nucleus, switching on genes for proliferation and survival.OUTSIDE THE CELLCYTOPLASMMEMBRANEkinasePPerlotinibkinasePPerlotinibGrb2·SOSRASRAFMEKERKNucleusgene transcription

Mechanism · animated schematic

How a growth-factor receptor switches on — and how a kinase inhibitor stops it

  1. 1A growth factor binds the extracellular domain of each receptor.
  2. 2Ligand-bound receptors pair up (dimerise) in the membrane.
  3. 3The two kinase domains phosphorylate tyrosines on each other (trans-autophosphorylation).
  4. 4Phosphotyrosines recruit adaptor proteins (Grb2·SOS), which activate RAS.
  5. 5RAS → RAF → MEK → ERK relays the signal to the nucleus, switching on genes for proliferation and survival.

Simplified schematic, not to scale; many more proteins take part. Based on Lemmon MA, Schlessinger J. Cell signaling by receptor tyrosine kinases. Cell 2010;141(7):1117–1134. doi:10.1016/j.cell.2010.06.011

Interactive · loads about 210 KB · PDB 1M17

Experimental structure · PDB 1M17

Erlotinib in the EGFR kinase domain

Erlotinib, an approved EGFR inhibitor, bound in the ATP pocket of the EGFR kinase domain. Its quinazoline ring sits against the hinge region, where the backbone of Met769 lies within hydrogen-bonding distance.

Measured contacts (≤ 3.5 Å, N/O atoms)

  • Met769 N — erlotinib N2: 2.7 Å
  • Pro770 O — erlotinib O4: 3.21 Å
  • Gly772 N — erlotinib O4: 3.24 Å
  • Leu694 O — erlotinib O2: 3.27 Å

Residues within 4.5 Å of the ligand

Leu694 · Val702 · Ala719 · Lys721 · Glu738 · Leu764 · Ile765 · Thr766 · Gln767 · Leu768 · Met769 · Pro770 · Phe771 · Gly772 · Leu820 · Thr830 · Asp831

X-ray diffraction, 2.6 Å resolution. Source: RCSB PDB 1M17 — Stamos, J., Sliwkowski, M.X., Eigenbrot, C. Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. J.Biol.Chem. 2002. doi:10.1074/jbc.M207135200

Distances were measured by Rehbar from the deposited coordinates (prepared 2026-10-16). They indicate likely hydrogen bonds; they are not an energy calculation, and this is published structural data — not Rehbar’s own experiment or a client result.

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Structures of nanobodies (green) bound to SARS-CoV-2 spike protein (magenta).
Goodsell · RCSB PDB · CC BY

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This painting includes three types of filaments that make up the cytoskeleton: a microtubule (the largest), an intermediate filament (the knobby one), and two actin filaments (the smallest ones). The large blue molecules are ribosomes , busy in their task of synthesizing proteins
Goodsell · RCSB PDB · CC BY

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