Percolator — semi-supervised machine learning tool for rescoring peptide-spectrum matches (PSMs) from shotgun proteomics database searches. Uses target-decoy competition with SVM classification to sep
Use with AI
Install the MCP server or CLI to instantly fetch Percolator documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/percolator
AlphaFold2 — deep learning system for predicting 3D protein structures from amino acid sequences with atomic-level accuracy. Uses multiple sequence alignments (MSAs) and an attention-based Evoformer a
2 shared topics • 1 shared operation
AlphaPept — Python-based, open-source proteomics pipeline for DDA mass spectrometry data analysis. Provides feature detection, peptide identification via database search, deep learning-based scoring,
2 shared topics • 1 shared operation
Use when working with mokapot — mokapot -- Python package for semi-supervised
2 shared topics • 1 shared operation
Prosit — deep learning framework for predicting MS2 fragment ion spectra and indexed retention times (iRT) from peptide sequences. Enables in silico spectral library generation for any organism and pr
2 shared topics • 1 shared operation
PyTorch Geometric (PyG) — graph neural network library built on PyTorch for learning on graphs and irregular structures. Provides message-passing layers (GCN, GAT, GraphSAGE, GIN, Transformer), mini-b
2 shared topics • 1 shared operation