Welcome to the CDD-Toolbox repository! This curated collection provides a comprehensive set of resources for Computational Drug Discovery (CDD) and related fields. Whether you are a researcher, student, or professional in the field of computational chemistry, this toolbox aims to serve as a valuable resource.
- Natural Compounds Libraries
- Chemical Bioactivity Databases
- 3D Protein Structures Databases
- Protein Engineering
- Binding Site Detection
- Pharmacophore Screening Tools
- Pharmacokinetics Parameters Prediction Tools
- QSAR modeling
- Topology Preparation
- Cheminformatics Free Courses
- Normal Mode Analysis for Predicting Protein Motions
- Virtual Screening Server for Drug Repurposing
- Peptide Design Tools
- PROTAC Database and Ternary Complex Modelling
- Miscellaneous tools
- Blogs
- COCONUT Natural Products - A database with more than 400k natural products compiled from over 50 sources.
- LOTUS Natural Products - Similar to COCONUT with a focus on molecular annotations, useful for sourcing organisms.
- ZINC15 Natural Products - A vast collection of >200k commercially available natural compounds for virtual screening.
- Collective Molecular Activities of Useful Plants - A database emphasizing molecular activities of beneficial plants.
- Natural Product Activity & Species Source Database (NPASS) - A database linking 94k natural product activities with their species sources.
- Cannabis Compound Database - A specialized database focusing on more than 6k compounds found in cannabis plants .
- SuperNatural III - A database offering information on natural compounds and their biological activities.
- FooDB - A comprehensive database of >70k food components, aiding in the exploration of the chemical composition of various foods.
- AfroDB - A database highlighting >4k compounds from African medicinal plants, contributing to research in ethnopharmacology and drug discovery.
- Comprehensive Marine Natural Products Database - A resource providing information on >31k marine-derived natural products.
- SistematX secondary metabolites database - A database focusing on >8k secondary metabolites.
- Eximed Natural-Product-Based Library - A collection of >5k natural product-like compounds designed for high-throughput screening in drug discovery.
- CoumarinDB - A database specifically focusing on some 900 naturally occuring coumarin compounds.
- ArtemisiaDB - A database dedicated to compounds from the genus Artemisia.
- OTAVA Natural Product-Like Library - A library of >1k natural product-like compounds designed for high-throughput screening in drug discovery.
- BIAdb - A database providing information on bioactive peptides and proteins with potential therapeutic applications.
- IMPPAT - A database focused on immunomodulatory peptides and proteins, supporting research in immunopharmacology.
- NP-MRD - A natural product database with a focus on >280k NMR studies.
- IBS Natural Compounds - A database providing information on >60k natural compounds.
- Phytochemicals - A comprehensive resource offering information on phytochemicals, supporting research in plant chemistry and pharmacology.
- ChEMBL database - A large-scale bioactivity database that focuses on bioactive molecules and their targets. It contains information on the binding, functional, and ADMET properties of drugs.
- BindingDB - A comprehensive database that provides information on the binding affinities of drugs to their target biomolecules.
- PubChem database - Offers information on the biological activities of small molecules, including chemical structures, properties, and bioassay data.
- PDBbind database - A database focusing on the experimentally measured binding affinities of biomolecular complexes. It includes data on protein-ligand complexes derived from the PDB, providing insights into the structures and energetics of protein-ligand interactions.
- BRENDA Enzymes database - A comprehensive enzyme information system that collects and provides data on enzyme function, structure, and properties. It covers a wide range of enzyme-related information.
- ExCAPE-DB: ExCAPE chemogenomics database - A chemogenomics database that integrates data on chemical compounds, protein targets, and biological activities.
- DrugBank - Provides comprehensive data on approved and investigational drugs, including details on chemical structures, pharmacology, and therapeutic indications.
- ZINC - A platform for researchers to explore and obtain compounds for various computational and experimental studies.
- ChemSpider - A free chemical database offering information on chemical structures, properties, and associated data.
- DrugSpaceX - A database designed to explore chemical and biological spaces related to drug discovery.
- RCSB Protein Data Bank - Global repository for biological macromolecule structures, facilitating research in structural biology and drug discovery.
- Protein Data Bank in Europe - European counterpart to RCSB PDB, providing deposition, retrieval, and analysis of macromolecular structures.
- Orientation of proteins in membranes database - Database focusing on spatial arrangements of integral membrane proteins, aiding understanding of their structural features.
- UniProt - Comprehensive resource combining protein sequences, structures, functions, and interactions, with links to 3D structures.
- InterPro - Integrated resource classifying proteins into families, predicting domains, and incorporating information from various protein databases.
- AlphaFold protein structure database - Database housing predicted protein structures generated by the AlphaFold deep learning system.
- Proteopedia - Collaborative web-based resource with interactive 3D visualizations providing information on protein structure and function.
- DynaMut - A web tool for the analysis and prediction of protein stability changes upon mutation using Normal Mode Analysis.
- ProteinsPlus - A tool designed for the identification and analysis of protein binding sites. It facilitates the exploration of protein-ligand interactions.
- PrankWeb - A web-based platform specializing in the prediction and analysis of protein binding sites.
- CASTp - A resource for the detection and characterization of protein binding sites. It offers insights into the volume and area of cavities on protein surfaces, contributing to the study of ligand binding and functional sites.
- CavityPlus - A web server designed for the identification and analysis of protein cavities and binding sites. It provides tools for the characterization of binding pockets, assisting researchers in studying protein-ligand interactions and structure-based drug design.
- ZINCPharmer - A web-based pharmacophore screening tool that facilitates the exploration of chemical databases. It aids researchers in identifying potential ligands based on pharmacophoric features.
- Pharmit - A pharmacophore modeling and virtual screening platform. It enables users to define and search for pharmacophoric patterns within chemical databases, assisting in the identification of compounds with specific bioactive properties for drug development.
- PharmMapper - A web server designed for pharmacophore mapping with statistical methods.
- SwissADME - A web tool for predicting pharmacokinetic parameters and drug-like properties. It assists researchers in assessing the drug-likeness and pharmacokinetic profile of small molecules. Supports multiple instances.
- pkCSM - A platform offering predictions for various physicochemical, pharmacokinetic and toxicity properties with the theory behind each prediction. Suitable for ADMET screening.
- ADMETlab 2.0 - A comprehensive tool for predicting absorption, distribution, metabolism, excretion, and toxicity properties of chemical compounds.
- ProTox-II - A predictive tool for assessing the toxicity endpoints of drugs.
- PreADMET - A web service providing predictions for pharmacokinetic properties. Does not support multiple instances.
- FAF-Drugs - A program designed to filter extensive compound libraries based on ADMET properties before in silico screening or modeling studies.
- QSAR Toolbox - The Toolbox is a free software for transparent chemical hazard assessment, offering tools for data retrieval, metabolism simulation, and property profiling. It aids in identifying analogues and chemical categories for read-across and trend analysis, filling data gaps.
- OCHEM - An online platform offering tools for building QSAR models for predictions of chemical properties.
- ChemMaster - A general cheminformatics software used to handle chemical data, in particular for drug design purposes including QSAR modeling.
- 3D-QSAR - A compilation of tools available online for 3D-QSAR modeling.
- CGenFF - Provides a force field parameterization platform for small organic molecules within the CHARMM force field. It assists researchers in preparing molecular topologies for use in molecular dynamics simulations.
- SwissParam - A tool for generating force field parameters for small molecules.
- Automated Topology Builder - A web-based tool for generating molecular topologies and force field parameters.
- CHARMM-GUI - A user-friendly interface for CHARMM, providing tools for the generation of molecular topologies and input files for simulations.
- Computational chemistry lectures by TMP Chem - A YouTube playlist offering computational chemistry lectures by TMP Chem. It covers various aspects of computational chemistry, providing valuable insights for learners interested in the field.
- Strasbourg Summer School in Chemoinformatics, 2022 - A YouTube playlist featuring lectures from the Strasbourg Summer School in Chemoinformatics. The content covers topics related to cheminformatics.
- BIGCHEM - The BIGCHEM project provides free courses on big data in chemistry. It offers online resources and training materials to explore the intersection of big data and chemistry, fostering understanding and skills in cheminformatics.
- iMod Server - A web-based platform dedicated to Normal Mode Analysis (NMA) for predicting protein motions. It allows researchers to analyze and simulate the vibrational modes of proteins, providing valuable insights into their dynamic behavior and structural flexibility.
- DrugRep - A virtual screening server designed for drug repurposing.
- PepDraw - A web-based tool for designing and visualizing peptide structures.
- PepSite - A peptide design tool that aids researchers in identifying potential binding sites on protein surfaces.
- Peptimap - A tool dedicated to the analysis and visualization of peptide structures.
- PROTAC-db - A database focused on Proteolysis Targeting Chimeras (PROTACs). It provides a resource for researchers interested in PROTACs by offering information on their design, targets, and associated experimental data, aiding in the exploration of targeted protein degradation.
- PROsettaC - A platform for ternary complex modeling, specifically focusing on the structural modeling of protein-protein interactions. It provides tools for predicting the three-dimensional structures of protein complexes, contributing to the understanding of PROTAC-induced ternary complexes and their implications in drug discovery.
- OPSIN: Open Parser for Systematic IUPAC nomenclature - Useful for converting chemical names into structured representations.
- OSRA: Optical Structure Recognition - An Optical Structure Recognition tool that converts graphical representations of chemical structures, such as images, into connection tables.
- PLIP - Protein ligand interaction profiler - A tool for profiling interactions between proteins and ligands. It helps analyze and visualize protein-ligand interactions, providing insights into molecular binding mechanisms.
- MetaPredict - A tool designed for predicting various molecular properties and activities. It supports computational chemistry by providing predictive models for diverse chemical entities.
- RPBS Web Portal - A platform offering a range of tools for computational biology and chemistry.
- AI based scoring function platform - Employs artificial intelligence to develop scoring functions for evaluating molecular interactions. It aids in predicting binding affinities and guiding drug discovery efforts.
- ChemPlot: A Tool For Chemical Space Visualization - A tool dedicated to visualizing chemical space.
- ChemDB Chemoinformatics Portal - A chemoinformatics portal offering various tools for chemical data analysis. It supports tasks such as compound search, similarity analysis, and property prediction.
- TorchDrug - A cheminformatics toolkit based on PyTorch. It provides functionalities for molecular property prediction, compound screening, and deep learning-based analyses.
- Open Targets Platform - The Open Targets Platform integrates genetic, genomic, and chemical data for target identification in drug discovery.
- Screening Explorer - A tool designed for compound screening and analysis.
- LigRMSD - A tool for calculating the root-mean-square deviation (RMSD) between ligand structures.
- BoBER: web interface to the base of bioisosterically exchangeable replacements - A web interface providing bioisosteric replacements for chemical structures.
- Disease List Automatically Derived For You - This tool automatically generates a list of diseases based on relevant data and criteria.
- Python Code Examples - Provide code snippets and examples for common tasks in the Python programming language. It's a valuable resource for learning and implementing Python in scientific computing.
- NERDD New E-Resource for Drug Discovery - A new e-resource focused on drug discovery. It provides information and tools to support researchers in the drug development process.
- MetaChemiBio - A tool designed for predicting molecular properties and activities.
- The Utrecht Biomolecular Interactions software portal - This portal provides software tools for studying biomolecular interactions.
- Spaya AI-powered retrosynthesis platform - An AI-powered platform for retrosynthetic analysis. It assists chemists in designing synthetic routes for target compounds.
- AutoDock Vina web server - A web-based interface for molecular docking simulations. It aids in predicting the binding modes of ligands to target proteins.
- CaverWeb: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport - A tool for identifying tunnels and channels in protein structures. It supports the analysis of ligand transport pathways.
- LigBuilder3 - A tool for building ligand structures and conducting virtual screening.
- MolAiCal - Useful for binding free energy calculations.
- ChemMine Tools - Provide a collection of cheminformatics and computational chemistry tools.
- Practical Fragments - A blog focusing on fragment-based drug discovery. It provides practical insights, case studies, and discussions on the use of small fragments in drug design.
- avrilomics - A blog covering topics in genomics, bioinformatics, and related fields. It offers insights, updates, and discussions on advancements and practical applications in these areas.
- Practical Cheminformatics - A blog dedicated to practical aspects of cheminformatics. It explores tools, techniques, and applications in the field of chemical informatics and computational chemistry.