Pharmacophore

• Roshambo: Open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules.
  

  

  

De Novo Generation

• PGMG: PGMG is a pharmacophore-guided deep learning approach for bioactive molecule generation, providing a strategy to generate molecules with structural diversity through the guidance of pharmacophore hypotheses.
  

  

  

From Apo Protein

• Apo2ph4: Workflow for the Generation of Receptor-based Pharmacophore Models for Virtual Screening (online).
  

• PharmRL:
  

  

From MD Simulations

• DynoPhores: DynoPhores introduces dynamic pharmacophore modeling of molecular interactions throughout MD simulations, tracking pharmacophore features and their interaction partners over time.
  

  

• PharMD: PharMD retrieves pharmacophore models from molecular dynamics (MD) trajectories of protein-ligand complexes, identifies redundant pharmacophores, and performs virtual screening using multiple pharmacophore models.
  

  

• Pharmmaker: Pharmacophore modeling model using outputs of druggability simulations. Uses multiple target conformations dependent on the binding poses of probes where they interact during druggability simulations (standalone and online).
  

Pharmacophore Model Generation

• AncPhore:

PyMol plugin

• OpenPharmaco: Open-source Protein-based Pharmacophore Modeling Software
  

  

Python

• 2DPharmSearch: 2DPharmSearch is a simple RDKit script for scaffold hopping experiments, utilizing 2D pharmacophore comparisons against a library of compounds to identify structurally similar molecules.
  

• ACP4: 3D-Sensitive Encoding of Pharmacophore Features (compare ligand in 3D or ligand-binding sites (holo structures) can compare pockets) (standalone)
  

  

• Align-it: Align-it is a tool for aligning molecules according to their pharmacophores, facilitating the comparison and matching of molecular structures based on pharmacophoric features.
  

  

• CDPKit Pharm:

• ConsensusPH4: This Jupyter notebook demonstrates the generation of consensus pharmacophore models, combining individual pharmacophore hypotheses to enhance virtual screening strategies.
  

  

• GRAIL: GRids of phArmacophore Interaction fieLds

  

• OpenPharmacophore: OpenPharmacophore is an open-source library aimed at working with pharmacophore models, deriving pharmacophores from ligand, ligand-receptor, receptor-based methods, and molecular dynamics trajectories.
  

• PMapper: PMapper is a Python module designed to generate 3D pharmacophore signatures and fingerprints, enabling fast identification of identical pharmacophores through unique hash encoding.
  

  

• PSearch: PSearch is a Python tool for generating 3D ligand-based pharmacophore models and performing virtual screening, facilitating the differentiation of active and inactive compounds via pharmacophore feature labeling.
  

  

• PharmRF: PharmRF introduces a new scoring function to select the best crystal structures for pharmacophore-based virtual screening, employing a random forest regressor to predict high-affinity ligands.
  

  

• PharmacoMatch: 3D Pharmacophore Screening through Neural Subgraph Matching
  

• PharmacoNet: PharmacoNet is designed for accelerating large-scale virtual screening by incorporating deep pharmacophore modeling, achieving rapid and reasonably accurate structure-based scoring.
  

  

• QPhar: QPhar provides code for quantitative pharmacophore activity relationship modeling, offering a method and validation for quantitative pharmacophore modeling documented in a publication.
  

  

• apo2ph4: apo2ph4 offers a versatile workflow for generating receptor-based pharmacophore models for virtual screening, focusing on the identification and utilization of pharmacophoric features derived from protein structures.
  

Screening

• PheSA: An Open-Source Tool for Pharmacophore-Enhanced Shape Alignment
  

  

Web-Servers

• Pharmit: Pharmit provides an interactive environment for the identification and visualization of pharmacophore models, enabling virtual screening against millions of compounds. It offers tools for specifying pharmacophores, flexibly searching chemical databases, and viewing results in 3D directly in the web browser.

  

  

VS, Docking

• DiffPhore: