Projects in Awesome Lists tagged with protein-sequences

https://github.com/songlab-cal/tape

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

benchmark dataset deep-learning language-modeling protein-sequences protein-structure pytorch semi-supervised-learning

Last synced: 09 Apr 2025

https://github.com/biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

bioinformatics genomics java parser-library pdb protein-data-bank protein-modification protein-sequences protein-structure sequence-alignment structural-bioinformatics structure-alignment

Last synced: 17 Dec 2025

https://github.com/microsoft/evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

discrete-diffusion generative-model multiple-sequence-alignment protein-sequences

Last synced: 14 May 2025

https://github.com/sacdallago/bio_embeddings

Get protein embeddings from protein sequences

bio-embeddings embedders language-model machine-learning pipeline protein-prediction protein-sequences protein-structure sequence-embeddings

Last synced: 08 Feb 2026

https://github.com/lucidrains/protein-bert-pytorch

Implementation of ProteinBERT in Pytorch

artificial-intelligence deep-learning protein-sequences unsupervised-learning

Last synced: 09 Apr 2025

https://github.com/oxpig/AbLang

AbLang: A language model for antibodies

antibodies language-model protein-sequences semantic

Last synced: 28 Apr 2025

https://github.com/flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

language-modeling neural-networks protein protein-sequences protein-structure sequence-alignment structural-alignments

Last synced: 10 Jul 2025

https://github.com/J-SNACKKB/FLIP

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

protein protein-design protein-fitness-prediction protein-function-prediction protein-sequences representation-learning

Last synced: 07 Apr 2026

https://github.com/songlab-cal/tape-neurips2019

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

benchmark dataset deep-learning language-modeling protein-sequences protein-structure semi-supervised-learning

Last synced: 07 May 2025

https://github.com/pengzhangzhi/faplm

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

protein-language-model protein-sequences pytorch

Last synced: 05 Apr 2025

https://github.com/rcedgar/usearch12

Open-source usearch

bioinformatics bioinformatics-algorithms computational-biology nucleotide-alignment protein-alignment protein-sequences search-algorithms

Last synced: 14 Jun 2025

https://github.com/tbepler/prose

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

deep-learning language-model protein-embedding protein-sequences representation-learning sequence-embedding

Last synced: 11 Sep 2025

https://github.com/seqan/lambda

LAMBDA – the Local Aligner for Massive Biological DatA

alignment bioinformatics blast blast-searches high-performance metagenomics ncbi-taxonomy protein-sequences seqan

Last synced: 28 Aug 2026

https://github.com/sbl-sdsc/mmtf-pyspark

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

apache-spark big-data binder jupyter jupyter-notebook machine-learning protein-data-bank protein-ligand-interactions protein-protein-interaction protein-sequences protein-structure pyspark scientific-computing

Last synced: 08 Sep 2025

https://github.com/pku-yuangroup/taxdiff

The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"

ai4science generate-model meachine-learning protein-sequences

Last synced: 07 May 2025

https://github.com/rcedgar/reseek

Protein structure alignment and search algorithm

bioinformatics bioinformatics-algorithms bioinformatics-tool computational-biology protein-sequences protein-structure search-algorithm

Last synced: 19 Apr 2025

https://github.com/ljvmiranda921/gym-lattice

An HP 2D Lattice Environment with a Gym-like API for the Protein Folding Problem

environments hp-model machine-learning protein-sequences protein-structure python reinforcement-learning

Last synced: 18 Oct 2025

https://github.com/nanxstats/protr

🧬 Toolkit for generating various numerical features of protein sequences

bioinformatics feature-engineering feature-extraction machine-learning peptides protein-sequences sequence-analysis

Last synced: 14 Mar 2026

https://github.com/genentech/walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

antibody machine-learning protein-design protein-sequences proteins

Last synced: 14 Apr 2025

https://github.com/OpenProteinAI/PoET

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

deep-learning generative-model protein-engineering protein-language-model protein-sequences proteins

Last synced: 01 May 2025

https://github.com/mims-harvard/SPECTRA

SPECTRA: Spectral framework for evaluation of biomedical AI models

benchmark-framework benchmarking foundation-models geometric-deep-learning large-language-models protein-language-model protein-sequences protein-structure

Last synced: 14 May 2026

https://github.com/nanxstats/rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

bioconductor bioinformatics cheminformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

Last synced: 22 Aug 2025

https://github.com/ericmjl/flu-sequence-predictor

An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.

bokeh deep-learning flask flu flu-forecaster gaussian-processes influenza influenza-protein-sequences protein-sequences pymc vaccine variational-autoencoders

Last synced: 13 Apr 2025

https://github.com/multiomics-analytics-group/course_protein_language_modeling

course education machine-learning protein-sequences slides

Last synced: 12 Apr 2025

https://github.com/fomightez/sequencework

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics list lists protein-sequences python rna

Last synced: 12 Apr 2025

https://github.com/opencog/agi-bio

Genomic and Proteomic data exploration and pattern mining

artificial-intelligence genetic-analysis genetics genomics protein-sequences proteomics

Last synced: 01 Mar 2026

https://github.com/dohlee/antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

antibody-sequence antibody-sequences bioinformatics biology protein protein-language-model protein-sequences

Last synced: 29 Apr 2025

https://github.com/openvax/pepnet

Neural networks for amino acid sequences

biological-data-analysis machine-learning neural-networks protein-sequences

Last synced: 27 Dec 2025

https://github.com/sbl-sdsc/mmtf-spark

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

apache-spark big-data machine-learning protein-data-bank protein-ligand-interactions protein-protein-interaction protein-sequences protein-structure scientific-computing

Last synced: 12 Apr 2025

https://github.com/hrzn/prot-gpt

Nano Prot GPT: NanoGPT on protein sequences

gpt protein-sequences pytorch

Last synced: 21 Aug 2025

https://github.com/feliixx/gotranseq

convert nucleic sequence in protein sequence

bioinformatics dna go protein-sequences translation

Last synced: 30 Apr 2025

https://github.com/slowikj/seqr

fast and comprehensive k-mer counting package

bioinformatics bioinformatics-tool dna-processing feature-engineering feature-extraction genomics hashing hashing-algorithms k-mer k-mer-counting kmer kmer-counting kmer-frequency-count kmers ngram ngrams protein-sequences rcpp rcppparallel rpackage

Last synced: 15 May 2025

https://github.com/amckenna41/protpy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

bioinformatics biological-data-analysis protein-sequences protein-structure protein-structure-prediction pypi pysar python

Last synced: 23 Aug 2025

https://github.com/kyegomez/progen

Implementation of the model from "ProGen: Language Modeling for Protein Generation"

artificial-intelligence attention-mechanism bioml gpt-4 protein-design protein-sequences

Last synced: 07 May 2025

https://github.com/gata-bio/affine-gaps

Less-wrong single-file Numba-accelerated Python implementation of Gotoh affine gap penalty extensions for the Needleman–Wunsch, Smith-Waterman, and Levenshtein algorithms for sequence alignment

bioinformatics jit levenshtein-algorithm levenshtein-distance needleman-wunsch protein protein-sequences search sequence-alignment smith-waterman string-search

Last synced: 12 Apr 2025

https://github.com/fomightez/blast-binder

Repo for running command line-based BLAST in Jupyter environment provided via Binder.

bioinformatics bioinformatics-analysis bioinformatics-scripts dna genomics pandas pandas-dataframe protein-sequences python rna

Last synced: 14 Jul 2025

https://github.com/pentalpha/protein_dimension_db

Datasets with embeddings and other representations for all proteins in Uniprot/Swiss-Prot

bioinformatics bioinformatics-databases dataset-generation gene-ontology plm plm-automation protein protein-function protein-language-model protein-sequences

Last synced: 15 May 2026

https://github.com/d-k-deng/protein_optimize

A software tool designed for protein optimization, ProteinOpti integrates sequence manipulation with structural analysis, streamlining the generation, prediction, and evaluation of protein variants using Google Colab.

bioinformatics google-colab ipynb protein-sequences

Last synced: 28 Oct 2025

https://github.com/dohlee/abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

bioinformatics biology computational-biology deep-learning protein protein-language-model protein-sequences protein-stability reproduction reproduction-code

Last synced: 14 Mar 2026

https://github.com/kklemon/protenc

Extract protein embeddings the easy way.

deep-learning drug-discovery protein-sequences

Last synced: 16 May 2025

https://github.com/pgarrett-scripps/fastaframes

Python package to convert between FASTA files and Pandas DataFrames.

bioinformatics fasta mass-spectrometry package pandas protein protein-sequences proteomics python

Last synced: 31 Jul 2025

https://github.com/fomightez/pdbepisa-binder

Using data from PDBePISA with the convenience of Python and Jupyter.

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics nucleic-acids nucleic-sequence pandas pandas-dataframe protein-sequences protein-structure python snakemake

Last synced: 31 Aug 2025

https://github.com/peptoneltd/dspp-data

Database of Structural Propensities of Proteins (dSPP) raw data repository by Peptone Inc.

biotechnology dataset keras keras-models machine-learning prediction protein protein-sequences protein-structure tensorflow tensorflow-models

Last synced: 12 May 2025

https://github.com/fomightez/patmatch-binder

Repo for running command line-based PatMatch in Jupyter environment provided via Binder.

bioinformatics bioinformatics-analysis dna pandas protein-sequences rna

Last synced: 11 Nov 2025

https://github.com/althonos/proteinogenic

Chemical structure generation for protein sequences as SMILES string.

bioinformatics chemical-structure protein-sequences rust-library smiles

Last synced: 07 Oct 2025

https://github.com/astrabert/proteins-w-esm

Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale

ai bioinformatics huggingface-spaces masked-language-models protein-sequences protein-structure structure-prediction

Last synced: 12 Apr 2025

https://github.com/iamazeem/ssic

Sequence Similarity and Identity Calculator (DNA + Protein)

bioinformatics biojava dna-sequences hacktoberfest java protein-sequences sequence-alignment

Last synced: 03 Apr 2025

https://github.com/dohlee/tranception-pytorch

Implementation of Tranception, a SOTA transformer model for protein fitness prediction, in PyTorch.

bioinformatics biology computational-biology deep-learning protein-sequences reproduction reproduction-code

Last synced: 29 Apr 2025

https://github.com/bob-friedman/protein-sequence-generation

Python code to help create a model protein sequence generation. Based on Huggingface transformers API and GPT-2 model.

bioinformatics protein-sequences pytorch

Last synced: 04 Apr 2026

https://github.com/astrabert/resistml

A tool for AMR gene family prediction, simple and ML-based

ai antibiotic-resistance bert-model finetuning healthcare machine-learning protein-sequences text-classification voting-classifier

Last synced: 16 Aug 2025

https://github.com/mg-rast/mym5nr

M5NRv2 -- non-redundant protein and rRNA database integration

protein-sequences rna-seq-data

Last synced: 27 Dec 2025

https://github.com/pgarrett-scripps/proteincleaverstreamlitapp

Protein Cleaver is a versatile tool for protein analysis and digestion.

digestion fasta mass-spectrometry peptide peptide-identification peptide-sequences peptides protein protein-sequences proteomics proteomics-data-analysis streamlit streamlit-cloud

Last synced: 15 Oct 2025

https://github.com/nanxstats/protrweb

Shiny Web Application for Protein Sequence-Derived Descriptor Computation

bioinformatics feature-extraction machine-learning protein-sequences

Last synced: 07 Mar 2026

https://github.com/smaniches/uniprot-mcp

Auditable UniProt MCP server with per-response SHA-256 provenance, release pinning, verification, and offline replay.

bioinformatics claude claude-ai claude-code clinvar-database clinvar-database-mcp drug drug-design drug-discovery drug-repurposing drug-target-interactions genomics mcp-server protein protein-protein-interaction protein-sequences protein-structure protein-structure-prediction uniprot

Last synced: 28 Aug 2026

https://github.com/odoluca/fast-nw-and-sw-pairwise-alignment-using-numba-jit

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

alignment cython dna-sequences gotoh needleman-wunsch numba pairwise pairwise-alignment protein-sequences pypy3 python python-3-6 smith-waterman

Last synced: 05 Jan 2026

https://github.com/fomightez/pdbsum-binder

Demonstrating analysis of PDBsum-related data via active Jupyter sessions provided via MyBinder.org

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts genomics pandas pandas-dataframes protein-sequences protein-structure python snakemake

Last synced: 30 Jan 2026

https://github.com/tusharpandey003/fasta-sequence-analysis-web-app

Analysis of FASTA ,Protein,DNA sequence.

bioinformatics biotechnology data-science dna-sequence-analysis dna-sequences fasta fasta-sequence fasta-sequences nucleotide-sequence protein-sequences sequence-analysis streamlit web-application

Last synced: 17 May 2026

https://github.com/ostrokach/uniparc_xml_parser

UniParc dataset describing ~300 million protein sequences converted into relational tables accessible through Google BigQuery (and as Parquet files).

bigquery bioinformatics csv-files parquet-files protein-domains protein-sequences

Last synced: 03 Jan 2026

https://github.com/aryaskov/kira-cluster

Deterministic Rust CLI for MMseqs2-like approximate high-throughput sequence clustering/search workflows

bioinformatics clustering protein-sequences proteomics

Last synced: 13 Aug 2026

https://github.com/madsondeluna/biohub

BioHub é uma ferramenta de linha de comando leve, prática e centralizadora, escrita em Python puro, para realizar análises bioinformáticas a partir de arquivos de estrutura de proteínas (PDB) e sequências de aminoácidos.

bioinformatics educational-project open-source pipeline protein-sequences structural-biology