Curated Compendium of Drug Discovery

 



Drug discovery is a multidisciplinary process that integrates biology, chemistry, pharmacology, and cutting-edge technologies to identify and develop new therapeutic agents. From target identification to lead optimization and clinical evaluation, each stage requires precision, innovation, and collaboration. A curated list of drug discovery resources provides researchers, students, and professionals with a structured pathway to explore advancements, tools, and strategies that shape modern therapeutics. This compilation serves as a gateway to understanding the evolution of drug discovery, recent breakthroughs, and future directions, fostering knowledge-sharing and accelerating translational research.

Databases and Chemical Libraries

General Compound Libraries

  • DrugBank - Comprehensive data on approved and investigational drugs.
  • ZINC - Free compounds for screening.
  • ChemSpider - Chemical structures and data.
  • DrugSpaceX - Chemical and biological spaces.
  • Mcule - Virtual screening platform with purchasable compounds.
  • Otava Chemicals - Screening compounds and building blocks.
  • Vitas-M Laboratory - Chemical libraries for HTS and lead discovery.
  • Eximed - 60k+ compounds for virtual screening.
  • OTAVA NP-like Library - Screening compounds for prompt delivery.
  • Ambinter - 40M+ compounds for HTS, building blocks, and a wide selection of fragments and natural products.

Natural Product Libraries

Bioactivity Databases


Target and Protein Data

Protein Structures

  • RCSB PDB - Repository for macromolecular structures.
  • PDBe - European counterpart to RCSB PDB.
  • OPM - Orientation of proteins in membranes.
  • UniProt - Protein sequences, structures, and functions.
  • InterPro - Protein classification and domain prediction.
  • AlphaFold DB - Predicted structures from AlphaFold.
  • Proteopedia - Interactive protein visualizations.

Binding Site and Pocket Detection

  • PrankWeb - Pocket prediction and analysis.
  • CASTp - Pocket geometry and volume analysis.
  • CavityPlus - Pocket detection and druggability.
  • CaverWeb - Tunnel and channel detection.
  • PASSer - Allosteric site prediction.

Protein Engineering and Modeling

  • DynaMut - Predicts mutation-induced stability changes.
  • SWISS-MODEL - A fully automated protein structure homology-modeling server.
  • MODELLER - A software for homology or comparative modeling of protein structures.
  • PDBFixer - Repairs PDB files by adding missing atoms, residues, and hydrogens for MD simulations.

Network Pharmacology

  • GeneCards - Human gene database with genomic, proteomic, and clinical data.
  • SwissTargetPrediction - Predicts targets of small molecules via similarity-based screening.
  • STITCH - Integrates chemical–protein interactions across organisms.
  • STRING - A database of known and predicted protein–protein interactions.
  • Cytoscape - Visualizes and analyzes molecular interaction networks.
  • Open Targets - Integrative platform for therapeutic target identification.
  • OmicsNet - Builds multi-omics networks for systems biology.
  • DisGeNET - Curated gene–disease associations for network analysis.
  • PharmMapper - Identifies potential targets via reverse pharmacophore mapping.
  • ChEA3 - Transcription factor enrichment tool integrating ChIP-seq, co-expression, and perturbation datasets.
  • miRDB - Predicts functional microRNA targets using machine learning and high-throughput data.
  • Venny 2.1 - A web tool for comparing lists using Venn diagrams.

Ligand Design and Optimization

Pharmacophore Modeling

  • ZINCPharmer - Pharmacophore screening.
  • Pharmit - Interactive pharmacophore modeling.
  • AnchorQuery - Pharmacophore-based search engine specialized in protein–protein interaction sites.

QSAR and Descriptor Tools

  • QSAR Toolbox - Hazard assessment and QSAR.
  • OCHEM - QSAR model building and prediction.
  • ChemMaster - QSAR and cheminformatics suite.
  • 3D-QSAR - 3D-QSAR modeling resources.
  • QSAR-Co - Robust multitarget QSAR modeling.
  • DataWarrior - Free software for chemical analysis, QSAR, and visualization.
  • KNIME - Workflow platform for cheminformatics and ML integration.
  • pyADA - Assesses the applicability domain of molecular fingerprints via similarity-based thresholds for QSAR validation.

Descriptor and Featurization Tools

  • RDKit - Open-source cheminformatics toolkit with descriptor, fingerprint, and molecular manipulation support.
  • PaDEL-Descriptor - Java tool for calculating molecular descriptors and fingerprints.
  • Mordred - Python library with 1800+ molecular descriptors.
  • CDK - Java cheminformatics library with descriptor calculators.
  • alvaDesc - Commercial software for molecular descriptors and fingerprints.
  • MolFeat - Python package for molecular featurization and embeddings.
  • Dragon - Commercial molecular descriptor calculator (widely cited).

Molecular Property Prediction

  • SwissADME - Drug-likeness and PK.
  • pkCSM - ADMET property prediction.
  • DeepPK - DL-based pharmacokinetics.
  • admetSAR 2.0 - Comprehensive ADMET.
  • ADMETlab 2.0 - PK, toxicity and drug-likeness.
  • ProTox-II - Toxicity predictions.
  • PreADMET - PK property predictions.
  • FAF-Drugs - ADMET filtering.
  • Admetboost - ML-based ADMET prediction.
  • MetaPredict - Predict molecular properties from structure.
  • ADMET-AI - A web-based tool for predicting ADMET properties based on Chemprop-RDKit models trained on datasets from the TDC.

Fragment-Based Drug Design

  • SwissSidechain - Fragment and linker library for small molecule design.
  • BoBER - Bioisosteric replacements for lead optimization.
  • FragBuilder - Python API for building peptide-like and small molecule fragments.
  • SeeSAR - Fragment growing and linking software (free academic version).
  • Enamine Fragment Libraries - Large curated collection of diverse fragments for FBDD.

Virtual Screening and Docking

  • OpenBabel - Format conversion and ligand prep.
  • Meeko - Prepares ligands/receptors for AutoDock by assigning partial charges and atom types.
  • MolScrub - Enumerates tautomers, pH states, and conformers for docking and structure-based modeling.
  • MGLTools - Structure preparation.
  • AutoDockTools - AutoDock GUI.
  • AutoDock Vina - Popular docking software.
  • AutoDock-GPU - GPU-accelerated version of AutoDock for faster ligand-receptor docking.
  • DiffDock - Deep learning-based docking tool that predicts ligand poses directly from protein structures using diffusion models.
  • EasyDockVina2 - Vina automation.
  • Webina - Web-based Vina.
  • Smina - Vina fork with extra features.
  • Gnina - CNN-scoring docking.
  • EasyDock - Vina/Smina pipeline.
  • HADDOCK - Flexible docking suite.
  • PandaDock - Python docking tool.
  • ZDOCK - Protein-protein docking.
  • ClusPro - Protein-protein docking server.
  • pyDockWEB - Electrostatics-based docking.
  • SwissDock - Web docking for beginners.
  • MzDOCK - GUI docking pipeline.
  • Uni-Mol Docking V2 - AI-assisted docking.
  • Vina on Colab - Run Vina in Google Colab.

Interaction Analysis and Visualization

  • PLIP - Protein-ligand interaction profiling.
  • LigPlot+ - 2D interaction diagrams.
  • Discovery Studio Visualizer - Advanced visualization.
  • PyMOL - Python-based molecular visualization software.
  • UCSF ChimeraX - A molecular visualization program with emphasis on structural biology.
  • Avogadro - Cross-platform molecular editor and visualizer featuring an extensible plugin system.

Molecular Dynamics and Simulation

Engines

  • GROMACS - Fast, scalable MD engine optimized for biomolecular simulations and energy minimization.
  • OpenMM - Flexible MD toolkit with GPU acceleration and Python bindings.
  • LAMMPS - Classical MD simulator for materials science and soft matter.
  • NAMD - Highly parallel MD engine tailored for large biomolecular systems.
  • AMBER - Suite for biomolecular simulations and free energy calculations.
  • Desmond - GPU-accelerated MD engine for high-performance simulations.

Topology and Force Field Tools

  • CGenFF - CHARMM force field parametrization of drug-like molecules.
  • SwissParam - Rapid generation of CHARMM-compatible parameters for small organic molecules.
  • ATB - Automated topology builder and repository for classical force field parameters.
  • CHARMM-GUI - Web-based interface for building complex biomolecular systems and generating MD input files.
  • LigParGen - Automated OPLS-AA parameter generator for organic ligands.

Analysis Tools

  • MD DaVis - Interactive visualization and analysis of MD trajectories.
  • iMod - Normal Mode Analysis toolkit using internal coordinates.
  • MolAiCal - Web-based platform for binding free energy calculations using MM/PBSA and MM/GBSA methods.
  • gmx_MMPBSA - Port of AMBER MMPBSA.py for GROMACS.
  • VMD - Large biomolecular systems visualization and analysis using 3D graphics and scripting.
  • Grace - 2D plotting tool for Unix-like systems with advanced graphing, fitting, and analysis features.
  • CPPTRAJ - Fast, parallelizable trajectory analysis from AMBER.
  • MDAnalysis - Open-source Python library for analyzing MD simulations.

Synthesis and Retrosynthesis Planning

  • Spaya - AI-driven retrosynthesis engine with route ranking and synthetic feasibility scoring.
  • AiZynthFinder - Monte Carlo tree search-based retrosynthesis using trained neural networks.
  • ASKCOS - Synthesis route prediction with ML, developed by MIT.
  • IBM RoboRXN - Automated reaction prediction using transformer models.
  • MANIFOLD - Search engine for synthetically accessible molecules and building blocks.

Specialized Modalities

PROTACs and Ternary Complexes

  • PROTAC-db - Curated database of PROTAC molecules, targets, and linkers for degrader design.
  • PROsettaC - Structure-based modeling of ternary complexes for targeted protein degradation.

Peptide Design

  • PepDraw - Peptide visualization with annotated physicochemical properties.
  • PepSite - Predict peptide binding sites on protein surfaces using structural data.
  • Peptimap - Peptide mapping and binding hotspots identification.

Machine Learning and AI

Core Libraries

  • scikit-learn - General-purpose ML library for classification, regression, clustering, and model evaluation.
  • PyTorch - Deep learning framework with extensive support for neural network modeling.
  • TensorFlow - End-to-end ML platform for scalable model development and deployment.
  • Keras - High-level neural network API running on top of TensorFlow, designed for fast experimentation.
  • NumPy - Core library for numerical computing with support for arrays, matrices, and linear algebra.
  • Pandas - Data manipulation and analysis toolkit built on top of NumPy.
  • Matplotlib - Comprehensive library for creating static, animated, and interactive visualizations in Python.
  • seaborn - Statistical data visualization library built on top of Matplotlib.

Chemistry-focused ML Frameworks

  • DeepChem - Open-source deep learning framework for chemistry and biology.
  • scikit-mol - Scikit-learn compatible cheminformatics extensions for molecular ML workflows.
  • Chemprop - Directed message passing neural networks for molecular property prediction.
  • ChemML - Machine learning and informatics suite for analyzing, mining, and modeling chemical and materials data.
  • Oloren ChemEngine - Unified API for molecular property prediction with uncertainty quantification, interpretability, and model tuning.
  • TorchDrug - A machine learning library for drug discovery with support for GNNs and molecular datasets.
  • DGL-LifeSci - Graph deep learning toolkit for life sciences using the Deep Graph Library.

Pretrained Models

  • MolBERT - Transformer-based molecular representation learning.
  • ChemBERTa - Pretrained BERT-like models for molecules from SMILES.
  • Uni-Mol - 3D molecular representation learning framework.
  • Boltz-2 - A foundation model that jointly predicts structure and binding affinity, rivaling physics-based FEP methods in accuracy.

AutoML and Optimization

  • Auto-sklearn - Automated machine learning for scikit-learn.
  • TPOT - Genetic programming-based AutoML for optimizing ML pipelines.
  • Optuna - Hyperparameter optimization framework for machine learning.

Molecule Standardization

  • MolVS - Molecule validation and standardization library based on RDKit.

Utility and Workflow Tools

  • ProteinsPlus - A web-based platform designed to assist life scientists in analyzing and working with protein structures.
  • OPSIN - Convert IUPAC names to chemical structures.
  • OSRA - Extract chemical structures from images.
  • ChemPlot - Chemical space visualization.
  • ChemDB - Chemoinformatics portal with compound data and tools.
  • Screening Explorer - Analyze screening datasets and hit distributions.
  • LigRMSD - Calculate RMSD between ligand poses.
  • NERDD - Curated drug discovery resources.
  • LigBuilder3 - De novo ligand design.
  • ChemMine Tools - Web-based cheminformatics toolkit for compound analysis.
  • MayaChemTools - Perl/Python scripts for cheminformatics.
  • Click2Drug - CADD software and databases directory.
  • Galaxy Europe - Galaxy instance for cheminformatics.
  • CADD Vault - CADD resources repository.
  • BioMoDes - Biomolecular structure prediction and modeling tools.
  • PlayMolecule - Interactive molecular modeling and simulation platform.
  • Ertl Molecular - Cheminformatics tools for medicinal chemists, including scaffold analysis, ring replacement, and property calculators.

Learning Resources

Free Courses

Blogs

Instructional Notebooks

Labs and Research Groups

  • Carlsson Lab - GPCR modeling, receptor-ligand interactions, MD, docking, and AI for drug discovery. (Uppsala University, Sweden)
  • InSiliChem - Computational chemobiology and metalloenzyme design. (Universitat Autònoma de Barcelona, Spain)
  • LCBC - Molecular dynamics, free energy calculations, retrosynthesis using machine learning. (Seoul National University, Korea)
  • Angelo Raymond Rossi - High-performance computing for computational chemistry and cheminformatics. (University of Connecticut, USA)
  • Laboratory of Chemoinformatics - QSAR/QSPR, chemical similarity, and virtual screening. (Université de Strasbourg / CNRS, France)
  • Erastova Lab - Molecular modeling of soft matter and biomolecular simulations. (University of Edinburgh, UK)
  • The Ballester Group - Developing ML/AI methods for structure-based scoring and virtual screening. (Imperial College London, UK)
  • Meiler Lab - Rosetta software, protein design, and ML-based protein engineering. (Vanderbilt / Leipzig University, USA / Germany)
  • COMP3D - Develops and applies AI methods to design safe, effective pharmaceuticals and agrochemicals. (University of Vienna, Austria)
  • Bonvin Lab - Computational structural biology, HADDOCK, and integrative modeling. (Utrecht University, Netherlands)
  • Volkamer Lab - Binding site analysis and AI-powered virtual screening. (Saarland University, Germany)
  • AI Laboratory for Molecular Engineering - PROTACs, molecular glues, and ML for chemistry and life sciences. (Chalmers University, Sweden)
  • Loschmidt Labs - PEG - Protein and enzyme engineering, AI-assisted enzyme design. (Masaryk University, Czechia)
  • QSAR4U - Cheminformatics tools, QSAR modeling, CReM, and EasyDock. (Palacky University, Czechia)




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