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

Open-source usearch

Inference of couplings in proteins and RNAs from sequence variation

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

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

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

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.

A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.