precise and accurate Identification of Native Proteoforms: a package for the supervised analysis of intact protein fragmentation data

Code for running RFdiffusion

List of papers about Proteins Design using Deep Learning

A software tool for fitting data from titration experiments.

Subset of AmberTools, with updates and modifications

random coil chemical shift predictor (JT Nielsen & FAA Mulder, 2018)

Chemical shift Secondary structure Population Inference

localCIDER - sequence analysis tool for disordered protein sequences

Multiple Protein Structure Alignment at Scale with FoldMason

A succinct wrapper for matplotlib

Collection of useful bioinformatic functions and tools for various computational biology pipelines

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

The codebase of the OpenMS project

Python Toolkit for Mass Spectrometry

BMRB data visualization tools using python Plotly

Code, 3D Print Files, BOM and Build Instructions for the DIYNAFLUOR DNA Fluorometer

A manually curated lists of software, publications and other resources related to the analysis of HDX-MS data.

Official repository for the Boltz biomolecular interaction models

MMseqs2: ultra fast and sensitive search and clustering suite

mzmine source code repository

AlphaFold 3 inference pipeline.

A trainable PyTorch reproduction of AlphaFold 3.

Open source implementation of AlphaFold3

A community dedicated to education of computer coding applied to mass spectrometry applications.

Universal Deconvolution of Mass and Ion Mobility Spectra

UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted f…

High accuracy RAG for answering questions from scientific documents with citations