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Search results for python protein

499 search results found

Deepdrug3d ⭐ 46

A convolutional neural network for classifying binding pockets based on spatial and chemical information extracted from the pockets.

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

View proteins and trajectories in the terminal

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

iLearn, a Python Toolkit and Web Server Integrating the Functionality of Feature Calculation, Extraction, Clustering, Feature Selection, Feature Normalization, Dimension Reduction and Model Construction for Classification, Best Model Selection, Ensemble Learning and Result Visualization for DNA, RNA and Protein Sequences.

Function prediction using a deep ontology-aware classifier

Vae_protein_function ⭐ 44

Protein function prediction using a variational autoencoder

Paired_cell_inpainting ⭐ 44

Self-supervised learning for microscopy images

Ensembler ⭐ 44

Automated omics-scale protein modeling and simulation setup.

Cell2cell ⭐ 44

User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins

Deepconv Dti ⭐ 43

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

Prismnet ⭐ 41

Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure

Pfeature ⭐ 41

A software package for computing features of peptides and proteins

Microbeannotator ⭐ 41

Pipeline for metabolic annotation of microbial genomes

Deepmind Alphafold Repl ⭐ 40

https://github.com/deepmind/deepmind-research

Smina Docking Benchmark ⭐ 40

Open Source Protein REdesign for You v3

Deepaccnet ⭐ 40

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

Macsyfinder ⭐ 38

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

Protlearn ⭐ 38

A Python package for extracting protein sequence features

Holoprot ⭐ 37

Multi-Scale Representation Learning on Proteins (NeurIPS 2021)

ProFET: Protein Feature Engineering Toolkit for Machine Learning

A python toolkit for analysing membrane protein-lipid interactions.

// PROJECT PAUSED FOR NOW (lack of capacity) // Protein cavity identification and automatic subpocket decomposition

Differentiable molecular simulation of proteins with a coarse-grained potential

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

Peptides.py ⭐ 36

Physicochemical properties, indices and descriptors for amino-acid sequences.

Localpdb ⭐ 36

Python package to manage protein structures and their annotations

Timed Design ⭐ 34

Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

Dips Plus ⭐ 34

The Enhanced Database of Interacting Protein Structures for Interface Prediction

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction (Briefings in Bioinformatics 2023)

Deepgoplus ⭐ 34

DeepGO with GOPlus axioms

Deepinteract ⭐ 33

A geometric deep learning pipeline for predicting protein interface contacts.

Graphsol ⭐ 33

Code of our JC paper: "Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map"

Omnipath ⭐ 32

Python client for the OmniPath web service

DLSCORE: A deep learning based scoring function for predicting protein-ligand binding affinity

Meta-Omics Software for Community Analysis

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

Ribosome Binding Site Calculator V1.0 ⭐ 31

The Ribosome Binding Site (RBS) Calculator can predict the translation initiation rate of a protein coding sequence in bacteria and design synthetic RBS sequences to rationally control the translation initiation rate. It is used to design synthetic biological systems.

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Deepdrug ⭐ 31

DeepDrug: A general graph-based deep learning framework for drug relation prediction

Open source biolab

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

Gopredsim ⭐ 29

PACKMAN: PACKing and Motion ANalysis

Fully convolutional neural networks for protein residue-residue contact prediction

Kaggle Human Protein Atlas Image Classification ⭐ 28

Kaggle 2018 @ Human Protein Atlas Image Classification

Pyentrezid ⭐ 28

Converts Ensembl, Uniprot, and HGNC IDs to Entrez Gene Id

Hotspots ⭐ 27

A knowledge-based method for determining small molecule binding "hotspots".

Phages2050 ⭐ 27

PHAGES2050 - a Comprehensive AI-based Framework for Phage Research & Therapy

Dbscan Swa ⭐ 27

Cogclassifier ⭐ 27

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Long Read Proteogenomics ⭐ 26

A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.

Pdb Benchmarks ⭐ 26

Benchmarking common tasks on proteins in various languages and packages

Protein Vae ⭐ 26

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

MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins

A tool for fast and accurate summarizing of variant calling format (VCF) files

Openawsem ⭐ 25

An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM

End-to-end deep learning toolkit for predicting protein binding sites and motifs.

Transfer Learning Bner Bioinformatics 2018 ⭐ 25

This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.

Protein Cascade Cnn Lstm ⭐ 25

Implementation of IJCAI15 cascade cnn and LSTM for protein secondary structure prediction

Fast and flexible ORF finder

Metasanity ⭐ 24

Pipeline for major biological analyses.

Biotrainer ⭐ 24

Taxon-aware analysis of clustered protein sequences

Broccoli ⭐ 24

orthology assignment using phylogenetic and network analyses

Onionnet ⭐ 24

A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction

Deepmetabolism ⭐ 24

DeepMetabolism is a deep learning algorithm to predict phenotype from genome sequencing

Miner Data ⭐ 24

Tcgaintegrator ⭐ 24

Python utilities for building integrated views of TCGA data.

Pdbcolor ⭐ 24

Python code to color a PDB structure based on parameters from a multiple sequence alignment

Deepsurf ⭐ 24

A surface-based deep learning approach for the prediction of ligand binding sites on proteins

Cryoem Cvpr2015 ⭐ 24

Source code to accompany the CVPR 2015 paper "Building Proteins in a Day"

Glycosylator ⭐ 23

Framework for the rapid modeling glycans and glycoproteins.

Deep Network Fusion (deepNF)

Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.

Modelling the Language of Life - Deep Learning Protein Sequences

Propkatraj ⭐ 23

pKa estimates for proteins using an ensemble approach

Electrostatics.github.io ⭐ 23

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

UniProt Id Mapping through API

Fragalysis ⭐ 22

A repo for analysis of ensembles of protein-ligand complexes

Rosalind ⭐ 22

Rosalind Bioinformatics Problems

Biostructmap ⭐ 22

A Python package for mapping sequence aligned data onto protein structures

a python module for generating protein contact maps and distance maps

Sequencework ⭐ 22

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

Frag_pele ⭐ 22

FragPELE, a new tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand conformational space

Swiftortho ⭐ 21

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

A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces

Git Repo for simulating Boolean Models

Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence

Dl4distanceprediction2 ⭐ 20

Python 3 implementation of Jinbo Xu's paper "Distance-based protein folding powered by deep learning", PNAS August 20, 2019 116 (34)

This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.

A software-suite to perform multiple protein structure alignment and structure feature extraction.

Predicting Drug Protein Interaction using Quasi-Visual Question Answering System

Vde_metadynamics ⭐ 20

Enhanced protein mutational sampling using time-lagged variational autoencoders

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