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

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

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Get protein embeddings from protein sequences

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

Implementation of ProteinBERT in Pytorch

AbLang: A language model for antibodies

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

Neural Networks for Protein Sequence Alignment

Inference of couplings in proteins and RNAs from sequence variation

Open-source usearch

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

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

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

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

Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies

LAMBDA – the Local Aligner for Massive Biological DatA

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.