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protein-sequences

Here are 167 public repositories matching this topic...

biojava / biojava

📖

🔬

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

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

Updated Apr 3, 2022
Java

songlab-cal / tape

Open

Extend list of models by SeqVec

1

ptynecki commented May 16, 2020

Hey,

I would propose extend list of available models by SeqVec (ELMo-based implementation) which was presented in the Modeling aspects of the language of life through transfer-learning protein sequences paper.

SeqVec model trained on UniRef50 is available at: [SeqVec-model](

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enhancement good first issue help wanted wontfix

bio_embeddings

sacdallago / bio_embeddings

Sponsor

Get protein embeddings from protein sequences

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

Updated Apr 8, 2022
HTML

williamgilpin / pypdb

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

proteins pdb protein-data-bank protein-structure protein-sequences proteomics blast

Updated Nov 1, 2021
Python

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

Updated Aug 7, 2021
Python

debbiemarkslab / plmc

Inference of couplings in proteins and RNAs from sequence variation

protein-structure protein-interaction protein-sequences undirected-graphs sequence-alignments

Updated Aug 18, 2020
C

seqan / lambda

LAMBDA – the Local Aligner for Massive Biological DatA

bioinformatics high-performance cpp14 metagenomics alignment protein-sequences ncbi-taxonomy blast blast-searches seqan

Updated Nov 7, 2021
C++

sbl-sdsc / mmtf-pyspark

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

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

Updated Jan 27, 2022
Python

lucidrains / protein-bert-pytorch

Sponsor

Implementation of ProteinBERT in Pytorch

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

Updated Aug 10, 2021
Python

psipred / protein-vae

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

protein-structure autoencoder protein-sequences topologies variational-autoencoder metal-binding-prediction

Updated Nov 26, 2019
Python

dosorio / Peptides

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

cran bioinformatics protein-sequences peptides calculate-indices qsar

Updated May 14, 2021
R

ljvmiranda921 / gym-lattice

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

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

Updated Mar 27, 2022
Python

pymodproject / pymod

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

bioinformatics pymol-plugin pymol protein-sequences sequence-alignments homology-modeling protein-structures structural-alignments similarity-searches

Updated Apr 8, 2022
Python

tbepler / prose

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

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

Updated Jun 16, 2021
Python

eliberis / parapred

Paratope Prediction using Deep Learning

python machine-learning neural-network protein-structure lstm protein-sequences lstm-neural-networks

Updated Feb 11, 2022
Python

nanxstats / protr

Comprehensive toolkit for generating various numerical features of protein sequences

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

Updated Dec 19, 2021
R

ericmjl / flu-sequence-predictor

Sponsor

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

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

Updated Feb 20, 2021
Jupyter Notebook

debbiemarkslab / EVzoom

Visually explore covariation in protein families

evolution protein-interaction protein-sequences undirected-graphs d3js amino-acids

Updated Dec 8, 2019
JavaScript

sagnikbanerjee15 / Finder

Open

Trouble running the example

56

josruirod commented Feb 11, 2021

Hi, and congratulations for the software. I want to give a try, and I managed to successfully install it (the conda environment and the step-by-step process is much appreciated, but there are few inaccuracies in the readme, such as FIND instead of find when running, or where is install.sh or the folder where the compressed files for the external software has to be downloaded).
When running the ex

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good first issue

flatironinstitute / deepblast

Open

Make GPU + CPU versions compatible

mortonjt commented Jul 3, 2020

We'll need to standardize the CPU / GPU version of needleman-wunsch.

Make sure that batching can be handled on the CPU (a hacked version is ok, will need to make sure that dimensions aren't an issue)
Make sure that the appropriate flags checking for devices are in place.

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good first issue

Open

More language models

Open

Loss functions

Find more good first issues

paulstothard / sequence_manipulation_suite

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.

protein-sequences molecular-biology sequence-analysis dna-processing

Updated May 20, 2021

conradry / pytorch-rgn

Recurrent Geometric Network in Pytorch

machine-learning proteins protein-structure pytorch protein-sequences

Updated Oct 14, 2020
Jupyter Notebook

amazon-sagemaker-protein-classification

aws-samples / amazon-sagemaker-protein-classification

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.

proteins protein-sequences distributed-training amazon-sagemaker bert-models amazon-sagemaker-studio protien-classification protbert-model sagemaker-distributed-data-parallel

Updated Feb 15, 2021
Jupyter Notebook

nanxstats / Rcpi

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

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

Updated Dec 22, 2021
R

openvax / pepnet

Neural networks for amino acid sequences

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

Updated Feb 26, 2018
Python

sbl-sdsc / mmtf-spark

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

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

Updated Feb 1, 2019
Java

ronakvijay / Protein_Sequence_Classification

A case study on Pfam dataset to classify protein families.

machine-learning bioinformatics deep-learning protein-sequences multiclass-classification

Updated Oct 10, 2019
Jupyter Notebook

Rinoahu / SwiftOrtho

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

genome cluster protein-sequences orthology-inference orthologs orthology-relationships paralogs

Updated Sep 29, 2020
Python

guyleonard / get_jgi_genomes

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

genome protein-sequences fungi algae genomes jgi mycocosm phytozome archaeplastida metazome jgi-genomes

Updated Oct 20, 2021
Perl

oxpig / AbLang

AbLang: A language model for antibodies

semantic protein-sequences language-model antibodies

Updated Mar 25, 2022
Python

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