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88 search results found

Proteinnet ⭐ 623

Standardized data set for machine learning of protein structure

Biojava ⭐ 564

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

Awesome Protein Representation Learning ⭐ 467

Awesome Protein Representation Learning

Bio_embeddings ⭐ 357

Get protein embeddings from protein sequences

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

Evodiff ⭐ 313

Generation of protein sequences and evolutionary alignments via discrete diffusion models

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

Protein Sequence Embedding Iclr2019 ⭐ 203

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

Dnanalyzer ⭐ 122

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

Official implementation of SaProt.

Tape Neurips2019 ⭐ 115

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

Inference of couplings in proteins and RNAs from sequence variation

AbLang: A language model for antibodies

Deepblast ⭐ 80

Neural Networks for Protein Sequence Alignment

Peptides ⭐ 71

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

LAMBDA – the Local Aligner for Massive Biological DatA

Mmtf Pyspark ⭐ 64

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

Protflash ⭐ 62

ProtFlash: A lightweight protein language model

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

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

Gym Lattice ⭐ 52

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

De novo protein structure prediction using iteratively predicted structural constraints

🧬 Toolkit for generating various numerical features of protein sequences

Sequence_manipulation_suite ⭐ 45

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.

A fully automated gene annotator from RNA-Seq expression data

Protein Bert Pytorch ⭐ 37

Implementation of ProteinBERT in Pytorch

Amazon Sagemaker Protein Classification ⭐ 35

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.

Flu Sequence Predictor ⭐ 34

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

MOLeculAR structure annoTator

Visually explore covariation in protein families

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Proteinfold ⭐ 26

Protein 3D structure prediction pipeline

Protein Vae ⭐ 26

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

Parapred ⭐ 25

Paratope Prediction using Deep Learning

Guided Conditional Wasserstein GAN for De Novo Protein Design

Sequencework ⭐ 22

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

Protein Localization Transformer ⭐ 22

Code for CELL-E: Biological Zero-Shot Text-to-Image Synthesis for Protein Localization Prediction

Swiftortho ⭐ 21

A high performance tool to identify orthologs and paralogs across genomes.

A Python 3 version of the protein descriptor package propy

Metagenomic Deepfri ⭐ 19

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Pytorch Rgn ⭐ 19

Recurrent Geometric Network in Pytorch

Mmtf Spark ⭐ 19

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

Walk Jump ⭐ 18

Official repository for discrete Walk-Jump Sampling (dWJS)

PyPEF – Pythonic Protein Engineering Framework

A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. PROST uses colab AlhpaFold2 for the prediction of pdb struture from FASTA sequence.

Neural networks for amino acid sequences

Deepcoil ⭐ 16

Fast and accurate prediction of coiled coil domains in protein sequences.

Protein orthologous group assignment with deep learning

Graph Part ⭐ 16

A biological sequence data partitioning method

Genomic and Proteomic data exploration and pattern mining

Get_jgi_genomes ⭐ 16

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Parapred Pytorch ⭐ 14

PyTorch implementation of Parapred (Liberis et al., 2018) with Paratyping (Richardson et al., 2021)

Protfeat ⭐ 13

ProtFeat is protein feature extraction tool that utilizes POSSUM and iFeature.

Protein Uq ⭐ 13

Benchmarking uncertainty quantification methods on proteins.

State-of-the-art ab initio prediction of 1D protein structure annotations

Proteinsolver ⭐ 12

Graph neural network capable of generating novel amino acid sequences that fold into proteins with predetermined topologies.

Gotranseq ⭐ 11

convert nucleic sequence in protein sequence

Prankwebapp ⭐ 11

Web application for protein-ligand binding sites analysis and visualization

Protein Feature Extraction ⭐ 10

Python code to extract features from Protein sequences for Machine Learning/Deep Learning

Deep learning based alignment-free method for protein family modeling and prediction

Cazy_webscraper ⭐ 10

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

Seqshuffle.jl ⭐ 9

Shuffle the string sequences such that the k-mer frequency is preserved in each string

Proteinfeatureview ⭐ 9

The Protein Feature View - a SVG library for visualising protein annotations

Pymissense ⭐ 9

PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.

Prion-Like Amino Acid Composition

A suite of unique bioinformatics tools for the brave explorer.

PyPEF – Pythonic Protein Engineering Framework

Prot Bo 0 ⭐ 8

💊 Guiding directed protein evolution with Bayesian Optimization 💊

fast and comprehensive k-mer counting package

Course_protein_language_modeling ⭐ 7

Aa_subtypes ⭐ 7

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

Python_scripts ⭐ 7

scripts for parsing PDB, fasta, and GO

Simple visualisation tool for sequences' similarity in bioinformatics

Caastools ⭐ 7

CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.

Covid Genome Computational Analysis ⭐ 6

Computational predictions of protein attributes associated with COVID-19 using Data Science techniques

Learning hierarchical motif representations for proteins.

Rosettasilenttoolbox ⭐ 6

Python Toolbox For Rosetta Silent Files Processing

Mhc Peptides Prediction ⭐ 6

A set of different models, that predict the degree of binding of peptide proteins.

Sequence Viewer ⭐ 6

A DNA and protein sequence viewer developed and maintained by Anocca

Blast Binder ⭐ 6

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

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

Genesdecypher ⭐ 5

A genetic decypher written in C. A school work of a student at Universidade Metodista de Angola.

Protein_optimize ⭐ 5

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.

A Deep Learning based protein flexibility prediction tool.

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

Protein_pretrain ⭐ 5

Multimodal Pretraining for Unsupervised Protein Representation Learning

Protein Coverage Summarizer ⭐ 5

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

1-88 of 88 search results

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