Proteomics

• AlphaFold3, https://github.com/google-deepmind/alphafold3
• AlphaFold Server, https://alphafoldserver.com/
• casanovo, https://github.com/Noble-Lab/casanovo
• CoffeeProt, https://coffeeprot.com/
• Consortium for Top-Down proteomics, https://www.topdownproteomics.org/
• DiaNN, https://github.com/vdemichev/DiaNN
• FINCHES-online, https://finches-online.com/ (https://github.com/idptools/finches)
• FreqPipe, https://fragpipe.nesvilab.org/
• Human Proteome Project (HPP), https://hupo.org/human-proteome-project (Resources, https://hupo.org/HPP-Resources)
• InstaNovo
  • GitHub, https://github.com/instadeepai/InstaNovo
  • HuggingFace, https://huggingface.co/spaces/InstaDeepAI/InstaNovo
    • High-confidence ProteomeTools dataset https://doi.org/10.57967/hf/3822
    • Nine species Benchmark, https://doi.org/10.57967/hf/3821
• ISA tools, https://isa-tools.org/
• KSEA, https://github.com/casecpb/KSEA
• MassIVE*¹, https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp?redirect=auth
• MassiveFold, https://github.com/GBLille/MassiveFold
• MaxQuant, https://maxquant.org/ (Mailing list)
• Mass++, https://mspp.ninja/download/
• MassBank of North America (MoNA)*, https://mona.fiehnlab.ucdavis.edu/
• MeMe, https://meme-suite.org/meme/index.html
• MetaboLights*, https://www.ebi.ac.uk/metabolights/index
• MS-GF+, https://msgfplus.github.io/
• OpenFold, https://openfold.io/
• Perseus, https://maxquant.net/perseus/
• Peptigram, http://bioware.ucd.ie/peptigram/
• PhosphoSitePlus, https://www.phosphosite.org/
• Protein Structure Prediction Center, https://predictioncenter.org/
• ProteomeXchange, https://www.proteomexchange.org/
• ProteoMapper Online, https://peptideatlas.org/map/
• R Programming for Mass Spectrometry
• RFdiffusion, https://github.com/RosettaCommons/RFdiffusion
• Sage, https://sage-docs.vercel.app/
• Sashimi, https://sourceforge.net/projects/sashimi
• Skyline, https://skyline.ms/project/home/begin.view
• Spectranaut, https://biognosys.com/software/spectronaut/