Dockamon

Dockamon is a computer-aided drug design (CADD) software offering pharmacophore modeling, 3D-QSAR, molecular docking, and other advanced tools. It combines comprehensive functionality with a modern, user-friendly interface, integrating both structure-based and ligand-based drug design methods into a single unified platform.

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Dockamon Interface

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Dockamon 1.2 - Basic

Provides a complete set of core features, allowing users to explore and evaluate the software.

  • Pharmacophore modeling (Basic)
  • 3D-QSAR modeling
  • Molecular Docking & Result Analysis (Single-Ligand)
  • Binding Site Detection (Convex Hull Method)
  • Ligand Scoring (Single Scoring Function)
  • Moelcular Alignment (Basic)
  • Other Features (Computing Propeties, Generating Conformers, etc.)

Free

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Dockamon 1.2 - Pro

Provides access to powerful CADD methods & algorithms, optimized for academic research and industrial projects.

  • Automatic Pharmacophore Model Detection
  • 4D-QSAR Modeling
  • Multiple-Ligands Docking
  • Advanced Alignment Method
  • Consensus Scoring (Multiple Scoring Functions)
  • Binding Site Detection (LigSite algorithm)
  • Commercial Use

$450.00

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Features

Dockamon - Basic Features

  • Pharmacophore Modeling
    • Common Features Model: Extract pharmacophore models from pre-aligned ligand sets
    • Manual Pharmacophore Models: Create custom models from ligand features or user-defined features
    • Model Validation: Validate models against ligand sets with metrics (accuracy, sensitivity, enrichment factor, ROC plots)
    • Customizable Features: Adjust SMARTS definitions and visualization colors
    • 2D/3D Visualization & Management: View and organize pharmacophore models
    • Export Models: Compatible with Pharmer (Pharmit webserver)
  • 3D-QSAR
    • Molecular Alignment: Multiple ligand alignment methods
    • Model Development & Validation: Automatic MIFs computation and model building
    • 3D-QSAR Visualization: Customizable 3D model visualization
    • Activity Prediction: Apply models to predict new ligands' activity
  • Molecular Docking & Rescoring
    • Single-Ligand Docking: Controlled docking/redocking (AutoDock Vina)
    • Result Analysis: 2D/3D interaction visualization & affinity data management
    • Protein/Ligand Preparation: Add hydrogens, remove fragments, etc.
    • Ligand Scoring: RF-Score V2 (machine-learning) for pose evaluation
  • Binding Site Detection
    • Convex Hull Algorithm: Fast binding site detection and scoring
    • Site Management: Visualize/manage sites in 3D; seamless docking integration
  • Molecular Alignment
    • Pharmacophore-Based Alignment: Align ligands by pharmacophore features
    • Open3DAlign: Algorithmic alignment of ligand sets
    • Alignment Management: Switch between alignments effortlessly
  • Additional Tools
    • Molecular Properties Calculation
    • 3D Conformer Generation: ETKDG method
    • Chemical Spreadsheet: Efficient ligand management with tabular operations
    • Modern UI: Integrated 3D viewer

Dockamon - Pro Features

  • Advanced Pharmacophore Modeling
    • Automatic Pharmacophore Detection: Uses an efficient recursive distance partitioning algorithm to detect pharmacophore models from active ligand sets
  • Virtual Screening by Pharmacophore
    • Pharmacophore-Based Screening: Screen compound libraries by matching structures to pharmacophore models
  • 4D-QSAR
    • Multi-Conformer QSAR: Models based on Molecular Fields Interactions (MFIs) with advanced visualization
  • Molecular Docking & Virtual Screening
    • Multi-Ligand Docking: High-throughput virtual screening powered by AutoDock Vina
  • Advanced Alignment Tools
    • Substructure-Based Alignment: Align structures via maximum common substructure (MCS)
  • Enhanced Scoring & Analysis
    • Consensus Scoring: Combine multiple scoring functions for robust pose evaluation
  • Binding Site Detection
    • LigSite Algorithm: Automatic binding site detection with LigSite

Dockamon 1.2 New Features