protein-sequences

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)

Implementation of ProteinBERT in Pytorch

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

AbLang: A language model for antibodies

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Neural Networks for Protein Sequence Alignment

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

Open-source usearch

Inference of couplings in proteins and RNAs from sequence variation

Inference of couplings in proteins and RNAs from sequence variation

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

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

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

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