This repository contains open resources for biomolecular data science.
The list includes:
- Open data resources
- Open data analysis and visualization tools
- Relevant open access scientific articles
- Relevant tutorials
Open data resources
- XTalkDB, Signaling Pathways (http://www.xtalkdb.org/download)
- Synaptic Physiology Dataset (https://portal.brain-map.org/explore/connectivity/synaptic-physiology/interact)
- wwPDB Worldwide Protein Data Bank (https://www.wwpdb.org/deposition/deposition-resources)
- AlphaFold Protein Structure Database, DeepMind and EMBL-EBI (https://alphafold.ebi.ac.uk/)
- UniProt Universal Protein Resource (https://www.uniprot.org/)
- InterPro Classification of protein families (https://www.ebi.ac.uk/interpro/)
- PDBe Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/)
- EMDB Electron Microscopy Data Bank (https://www.ebi.ac.uk/emdb/)
- IntAct Molecular Interaction Database (https://www.ebi.ac.uk/intact/home)
- Complex Portal Macromolecular complexes (https://www.ebi.ac.uk/complexportal/home)
- Reactome Pathway Database (https://reactome.org/)
- MatrixDB Extracellular Matrix Interaction Database (http://matrixdb.univ-lyon1.fr/)
- Expasy Swiss Bioinformatics Resource Portal (https://www.expasy.org/)
- The Human Protein Atlas (http://www.proteinatlas.org/)
- CATH Protein domains (http://www.cathdb.info/)
- ELIXIR Data resources (https://elixir-europe.org/services/tag/data-resources)
- IMEx The International Molecular Exchange (http://www.imexconsortium.org/)
Open data analysis and visualization tools
- Gephi (https://gephi.org/)
- Cytoscape (https://cytoscape.org/index.html)
- GraphSpace (https://graphspace.org/index)
Relevant open access scientific articles
- Visualization of Biomedical Data (Google Drive: https://bit.ly/3x8xdNl)
- The Levin Lab, Tufts University (https://ase.tufts.edu/biology/labs/levin/)
- Porras et al (2022) IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. Methods in Molecular Biology, 2449:27-42. (https://europepmc.org/article/MED/35507258)