Making Protein folding accessible to all!

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

Evolutionary couplings from protein and RNA sequence alignments

nucleic acid folding

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

PSP is a python toolkit for predicting atomic-level structural models for a range of polymer geometries.

Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale

Your open-source alternative to AlphaFold3🚀

Python bindings for the `buildcell` program for Ab Initio Random Structure Searching (AIRSS)

Recommendation-based Basin-Hopping for cation ordering optimization

Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.

deep learning based prediction of structures and functional groups from MS/MS spectra

A pipeline for AlphaFold2-Multimer on a SLURM compute cluster with visualization in ChimeraX.

[ACL 2023] SPEECH: Structured Prediction with Energy-Based Event-Centric Hyperspheres

Searching proteins against a database of embeddings

Protein Secondary Structure predictor using Convolutional Neural Networks

[EMNLP 2022] Generative Knowledge Graph Construction: A Review

[ACL'23 main] DICE: Data-Efficient Clinical Event Extraction with Generative Models

spdkit: Structure Predication Development Kit

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation