Molecular Docking & Screening
Deploy high-performance computer-aided drug design pathways. We identify ligand binding poses, calculate structural coordinates, and screen compound libraries against target proteins with strict academic rigor.
Virtual Screening & Pose Verification
Structure-based computer-aided drug design requires meticulous receptor preparation and exact conformation mapping. Our molecular docking pipelines are designed to support virtual screening campaigns and hit-to-lead optimization projects.
We evaluate free energy calculations using advanced MM-GBSA (Molecular Mechanics Generalized Born Surface Area) protocols to sort binders from non-binders.
Docking Pipelines We Deploy
- Receptor Struct Prep: Protonation state determination, ligand removal, grid center mapping.
- Ligand Libraries Prep: SMILES enumeration, 3D conformation generation, charge assignment (AM1-BCC).
- AutoDock Vina Docking: High-performance conformational search and binding affinity scoring.
- Pose Post-Processing: 2D interaction mapping (hydrogen bonds, salt bridges), PyMOL session generation.
The Molecular Docking Pipeline
Detailed checkpoints inside our compound evaluation and pose ranking workflows.
Receptor & Grid Preparation
PDB / fpocketIngest structures from the Protein Data Bank (PDB). Resolve missing loops, optimize hydrogen-bonding networks, and define the active site grid coordinates utilizing pocket search algorithms.
Ligand Conformation Generation
SMILES / RDKitGenerate 3D coordinates from chemical SMILES inputs. We enumerate appropriate tautomers, stereoisomers, and protonation states at physiological pH 7.4.
Conformational Docking Simulation
AutoDock VinaPerform flexible ligand-docking calculations. AutoDock Vina sweeps the binding pocket, identifying key energy minima poses and ranking compound binding affinities.
Interaction Mapping & Delivery
PyMOL / PLIPGenerate high-resolution 2D and 3D pocket maps detailing hydrogen bonds, hydrophobic contacts, and salt bridges. Deliver ranked compound PDB/SDF outputs, scoring matrices, and PyMOL visualization files.
Docking Inquiries
Yes. While non-covalent protein-ligand docking constitutes our standard pipeline, we build customized covalent docking steps (targeting cysteine or serine binding residues) as well as protein-protein docking models (utilizing HADDOCK or ClusPro algorithms). Please indicate this requirement in your project briefing.
You receive the fully prepared receptor structure, raw conformational docked complex files in PDB/SDF formats, an Excel scoring matrix detailing binding energies (kcal/mol), 2D interaction mapping diagrams, high-resolution PyMOL `.pse` layout sessions with preset viewpoints, and a detailed PDF methodology report suitable for patent filings or manuscript submissions.