#

proteins

Here are 172 public repositories matching this topic...

aqlaboratory / proteinnet

Standardized data set for machine learning of protein structure

machine-learning deep-learning proteins protein-structure dataset protein-sequence

Updated Nov 18, 2020
Python

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

biolib / openprotein

A PyTorch framework for prediction of tertiary protein structure

proteins protein-structure

Updated Jun 8, 2021
Python

bio4j / bio4j

Bio4j abstract model and general entry point to the project

Updated Dec 16, 2016
Java

HannesStark / EquiBind

Open

Potential improvement through avoiding DGL TensorDispatcher error

1

PatWalters commented Feb 28, 2022

I encountered this error when running Equibind.

/opt/dgl/src/runtime/tensordispatch.cc:43: TensorDispatcher: dlopen failed: libtorch_cuda.so: cannot open shared object file: No such file or directory

According to this https://discuss.dgl.ai/t/error-tensordispatcher/2468 the error impacts performance but does not impact usage. Equibind appears to run in spite of this error. I thought you m

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good first issue

plass

soedinglab / plass

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

opensource bioinformatics proteins metagenomics proteomics sequence-assembler metatranscriptomics

Updated Jan 14, 2022
C

Acellera / moleculekit

MoleculeKit: Your favorite molecule manipulation kit

machine-learning proteins molecule molecular-simulation drug-discovery molecular-modeling

Updated Mar 3, 2022
Python

rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

machine-learning bioinformatics proteins pdb protein-structure prediction protein-ligand-interactions binding-sites ligand inverse-virtual-screening protein-surface structural-bioinformatics

Updated Feb 3, 2022
Groovy

samirelanduk / atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

chemistry biology proteins structural-biology molecules

Updated Feb 2, 2022
Python

lucidrains / progen

Implementation and replication of ProGen, Language Modeling for Protein Generation, in Jax

deep-learning proteins artificial-intelligence

Updated Sep 8, 2021
Python

diegozea / MIToS.jl

Open

Increase test coverage to 95%

diegozea commented Oct 17, 2017

Actual test coverage is ~89%. That's great! However, would be great to increase that number to make this package more reliable and avoid future regressions ;)

It's easy to see what lines are missing tests using codecov and coveralls.

We need to find a way to test `MIToS

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help wanted good first issue

Open

Make use of PkgBenchmark

Open

MIToS should avoid `push!` calls

1

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PDB-REDO / dssp

Application to assign secondary structure to proteins

proteins pdb dssp

Updated Feb 13, 2022
C++

saezlab / OmnipathR

R client for the OmniPath web service

proteins networks pathways complexes networks-biology omnipath enzyme-ptm

Updated Feb 23, 2022
R

mircare / Porter5

Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes

machine-learning deep-learning proteins secondary-structure psi-blast protein-structure-prediction hhblit

Updated May 21, 2020
C++

sigven / oncoEnrichR

Cancer-dedicated gene set interpretation

cancer proteins disease-gene-association tcga-data crispr-target protein-protein-interaction co-expression report-generator prioritization genesets high-throughput-screening cancer-survival functional-enrichment-analysis pathway-enrichment-analysis protein-complexes tissue-enrichment-analysis cancer-hallmark-evidence

Updated Mar 2, 2022
R

psipred / psipred

PSIPRED Protein Secondary Structure Predictor

proteins secondary-structure-prediction

Updated Sep 17, 2021
Java

aqlaboratory / pnerf

machine-learning proteins protein-structure molecular-dynamics molecular-simulation molecular-modeling

Updated Jul 22, 2019
Python

conradry / pytorch-rgn

Recurrent Geometric Network in Pytorch

machine-learning proteins protein-structure pytorch protein-sequences

Updated Oct 14, 2020
Jupyter Notebook

BioinfoMachineLearning / DeepInteract

A geometric deep learning pipeline for predicting protein interface contacts.

docker machine-learning bioinformatics deep-learning proteins transformers geometric-deep-learning graph-neural-networks protein-protein-interactions

Updated Mar 4, 2022
Python

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

haddocking / haddock3

The official repo of the new modular BioExcel2 version of HADDOCK

bioinformatics proteins python3 modelling docking workflows complexes integrative-modeling utrecht-university

Updated Mar 4, 2022
Python

lightdock-python2.7

lightdock / lightdock-python2.7

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

bioinformatics simulation proteins pdb protein-structure dna protein scientific-computing swarm docking protein-protein nose peptides protein-design protein-protein-interaction receptor ligand mpi4py swarm-intelligence gso protein-protein-docking anm protein-docking-framework

Updated Mar 26, 2020
C++

pmartR / pmartR

The pmartR R package provides functionality for quality control, normalization, exploratory data analysis, and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data. This includes data transformation, specification of groups that are to be compared against each other, filtering of feature and/or samples, data normalization, and data summarization (correlation, PCA).

proteins mass-spectrometry peptides metabolites metabolomics-data data-summarization lipids

Updated Mar 3, 2022
R

BioinfoMachineLearning / DIPS-Plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction

machine-learning bioinformatics deep-learning proteins datasets

Updated Feb 11, 2022
Python

mircare / Brewery

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

machine-learning deep-learning proteins protein-structure protein-sequences hhblits secondary-structure psi-blast solvent-accessible-surface-area contact-density torsion-angles

Updated Feb 28, 2021
C++

tekpinar / correlationplus

A Python package to calculate, visualize and analyze correlation maps of proteins.

visualization python bioinformatics chemistry graph analysis proteins network dynamics centrality correlations diffmap

Updated Feb 28, 2022
Python

debbiemarkslab / MuE

A package for making MuE observation models in Edward2.

machine-learning proteins tensorflow probabilistic-programming biological-sequences

Updated Jun 10, 2021
Python

geometricus

TurtleTools / geometricus

A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

machine-learning proteins protein-structure feature-engineering alignment-free invariant-features

Updated Feb 23, 2022
Jupyter Notebook

psipred / disopred

Protein structural disorder prediction

proteins disorder-prediction

Updated Oct 12, 2017
C++

FarSeer-NMR

Farseer-NMR / FarSeer-NMR

A software suite for automatic treatment, analysis and plotting of large and multivariable datasets of bioNMR peaklists.

proteins protein-structure nmr protein-protein-interaction biomolecular

Updated Apr 17, 2020
Python

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