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

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

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

Awesome Protein Representation Learning

Get protein embeddings from protein sequences

Generation of protein sequences and evolutionary alignments via discrete diffusion models

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Inference of couplings in proteins and RNAs from sequence variation

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

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

Genomic and Proteomic data exploration and pattern mining

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

Protein 3D structure prediction pipeline

Implementation of ProteinBERT in Pytorch

AbLang: A language model for antibodies

Implementation of Protein Classification based on subcellular localization using ProtBert(Rostlab/prot_bert_bfd_localization) model from Hugging Face library, based on BERT model trained on large corpus of protein sequences.

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.

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

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

LAMBDA – the Local Aligner for Massive Biological DatA