Awesome Computational Biology

A knowledge collection of databases, software and papers related to computational biology.

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to the study of biological, ecological, behavioural, and social systems. - Wikipedia

Contents

• Databases
  • Compound
  • Pathway
  • Mass Spectra
  • Protein
  • Genome
  • Disease
  • Interaction
• Preprocess
• Machine Learning Tasks and Models
  • Drug Repurposing
  • Drug Target Interaction
  • Compound Protein Interaction

Databases

Compound

• PubChem - One of the biggest chemical database such as compounds, genes and proteins.
• ChEBI - Chemical database focused on small chemical compounds.
• ChEMBL - Database of bioactive molecules with drug-like properties.
• ChemSpider - Chemical structure database.
• KEGG COMPOUND - Collection of small molecules and biopolymers.
• LIPID MAPS - Database of lipids.

Pathway

• PathwayCommon - Database of Pathways and Interactions.
• KEGG PATHWAY - Collection fo drawn pathway maps.
• WikiPathways - Database of biological pathways.

Mass Spectra

• MassBank - Open souce databases and tools for mass spectrometry reference spectra.
• MoNA MassBank of North America - Meta database of metabolite mass spectra, metadata and associated compounds.

Protein

• THE HUMAN PROTEIN ATLAS - One of the biggest human protein database contained cells, tissues, and organs.
• PROTEIN DATA BANK - Database of the 3D shapes of proteins, nucleic acids, and complex assemblies.
• UniProt - The collection of functional information on proteins.

Genome

• Human Genome Resources at NCBI - Database of image, proteomics, transcriptomics and systems biology.
• GenBank - Database of genetic sequence offered by NCBI.
• UCSC Genome Browser - Genome blowser offered by UCSC.

Disease

• KEGG DRUG - Comprehensive drug information resource for approved drugs.
• DrugBank - A database of drug and target maintained by the University of Alberta.

Interaction

• Drug Gene Interaction
  • DGIdb - A database of drug-gene interactions and the druggable genome.
  • Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.
• Chemical Protein Interaction
  • STITCH - A database of Chemical Protein Interaction.

Preprocess

• Chemistry Development Kit - A software of cheminformatics and Machine Learning.
• RDKit - A software of cheminformatics and Machine Learning.

Machine Learning Tasks and Models

Drug Repurposing

• DeepPurpose - A DL Library for Drug Repurposing and so on.
• DRKG - A library for biological knowledge graph.

Drug Target Interaction

• NeoDTI - A library for Drug Target Interaction.

Compound Protein Interaction

• MCPINN - A library for drug discovery using Compound Protein Interaction and Machine Learning.
• TransformerCPI - A library for Compound Protein Interaction prediction using Transformer.