Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

Awesome Protein Representation Learning

Generation of protein sequences and evolutionary alignments via discrete diffusion models

📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Get protein embeddings from protein sequences

A Python API for the RCSB Protein Data Bank (PDB)

FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

AbLang: A language model for antibodies

Implementation of ProteinBERT in Pytorch

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Neural Networks for Protein Sequence Alignment

Open-source usearch

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

Inference of couplings in proteins and RNAs from sequence variation

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!

Multi-task and masked language model-based protein sequence embedding models.

Protein 3D structure prediction pipeline

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Inference code for PoET: A generative model of protein families as sequences-of-sequences