A Comparative Genomics Framework Integrating Synteny Visualization

pDeepXL: MS/MS spectrum prediction for cross-linked peptide pairs by deep learning

Neural Networks for Protein Sequence Alignment

Foldseek enables fast and sensitive comparisons of large structure sets.

Rapid & standardized genome annotation using protein structural information

The codebase of the OpenMS project

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer

A python package to process protein cross-linking data.

Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.

A search engine for the identification of cross-linked protein complexes or proteomes from mass spectrometry data.

A cross-platform proteomics data analysis suite

Converts a Thermo .raw file with FAIMS scans into a series of .mzXML files, creating one .mzXML file for each FAIMS compensation voltage (CV) value.

Repository for mzIdentML and the corresponding examples

Rescoring and spectral library generation pipeline for proteomics.

A web-based collaborative LaTeX editor

Report processing and protein quantification for MS-based proteomics

An S3 data object and framework for common quantitative proteomic analyses

DIA-NN - a universal automated software suite for DIA proteomics data analysis.

Making Protein folding accessible to all!