Informatics

Proteomics

• Skyline: https://skyline.ms/project/home/begin.view?

• MaxQuant & Perseus: https://www.maxquant.org/

• MSFragger: https://msfragger.nesvilab.org/

• Single-cell: https://scp.slavovlab.net/

Interactome

• STRING: https://string-db.org/

• HuRI: http://www.interactome-atlas.org/

• BioGRID: https://thebiogrid.org/

• IntAct: https://www.ebi.ac.uk/intact/home

• MINT: https://mint.bio.uniroma2.it/

• BioPlex: https://bioplex.hms.harvard.edu/explorer/home

• CORUM: https://mips.helmholtz-muenchen.de/corum/#

• HINT: http://hint.yulab.org/

• iRefWeb: https://wodaklab.org/iRefWeb/

• Mentha: https://mentha.uniroma2.it/index.php

• GPS-Prot: http://gpsprot.org/

• Wiki-Pi: http://severus.dbmi.pitt.edu/wiki-pi/

• PIPs: http://www.compbio.dundee.ac.uk/www-pips/

• HumanNet: https://staging2.inetbio.org/humannetv3/

• OmniPath: https://omnipathdb.org/

Network

• Cytoscape: https://cytoscape.org/

• Metascape: https://metascape.org/gp/index.html#/main/step1

• inBio Discover: https://inbio-discover.com/

Function

• DAVID: https://david.ncifcrf.gov/home.jsp

Pathway

• KEGG: https://www.genome.jp/kegg/

• Reactome: https://reactome.org/

• WikiPathways: https://www.wikipathways.org/

Structure Prediction

• PyMOL: https://pymol.org/2/

• PyMOLWiki: https://pymolwiki.org/index.php/Main_Page

• Protein Contacts Atlas: http://pca.mbgroup.bio//index.html

• CoLabFold: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb

Molecular Docking Simulation

• AutoDock: https://autodock.scripps.edu/

• HADDOCK: https://www.bonvinlab.org/software/bpg/peptides/

Homology Modeling

• SWISS-PROT: https://swissmodel.expasy.org/

• HHPred: https://toolkit.tuebingen.mpg.de/tools/hhpred

• I-TASSER: https://zhanggroup.org/I-TASSER/

Machine Learning

• Colab: https://colab.research.google.com/notebooks/intro.ipynb?utm_source=scs-index

• AutoML: https://cloud.google.com/automl-tables/docs

• TensorFlow: https://www.tensorflow.org/?hl=ko

• RapidMiner: https://rapidminer.com/

Biostatistics / Bioinformatics

• R-project: https://www.r-project.org/

• RStudio: https://rstudio.com/

• BioConductor: http://www.bioconductor.org/

• Anaconda: https://www.anaconda.com/

• Python: https://www.python.org/

• BioPython: https://biopython.org/

• BioRender: https://biorender.com/

• InstantClue: http://www.instantclue.uni-koeln.de/

• GNU PSPP: https://www.gnu.org/software/pspp/

• jamovi: https://www.jamovi.org/

• JASP: https://jasp-stats.org/

Mutation

• AlphaMissense: https://github.com/google-deepmind/alphamissense

ETC

• Uniprot Retrieve/ID mapping: https://www.uniprot.org/id-mapping

• Venn Diagram: https://eulerr.co/