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499 search results found

Qfit 3.0 ⭐ 20

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.

Predicting Drug Protein Interaction using Quasi-Visual Question Answering System

KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Reactomepy ⭐ 19

Explore biomolecular pathways in Reactome from the command-line or a Python script

Cryptosite ⭐ 19

Library for prediction of cryptic binding sites

iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines

Deepdist ⭐ 19

Deep learning prediction of protein residue-residue distances

TIP: Tri-graph Interaction Propagation model for Polypharmacy Side Eﬀect Prediction (GRL@NeurIPS, 2019)

Paccmann_proteomics ⭐ 19

PaccMann models for protein language modeling

Multitask Learning Protein Prediction ⭐ 19

Multitask learning: protein secondary structure prediction, b-values prediction and solvent-accessibility prediction

Shortbred ⭐ 19

ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.

Probabilistic Graphical Models in Python3.

Correlationplus ⭐ 18

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

Walk Jump ⭐ 18

Official repository for discrete Walk-Jump Sampling (dWJS)

Protocaller ⭐ 18

Full automation of relative protein-ligand binding free energy calculations in GROMACS

Pinnacle ⭐ 18

Contextualizing protein representations using deep learning on protein networks and single-cell data

Kaggle Hpa ⭐ 18

Kaggle Human Protein Atlas Image Classification 73th solution

Paw_pipeline ⭐ 18

A Comet-based, best practices proteomics pipeline.

Noise2noise Cryo Em Image Denoising ⭐ 18

pytorch implementation of noise2noise for Cryo-EM image denoising

Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor

A machine-learning package for navigating combinatorial protein fitness landscapes.

Neurips19 Graph Protein Design ⭐ 18

Generative Models for Graph-Based Protein Design

De novo VIral Genome Annotator

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

A toolkit to validate and consolidate antimicrobial resistance gene databases

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

Genome_collector ⭐ 17

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

Capsnet_ptm ⭐ 17

CapsNet for Protein Post-translational Modification site prediction.

Diffnets ⭐ 17

Self-supervised neural nets to understand protein mutations

The triqler (TRansparent Identification-Quantification-linked Error Rates)'s source and example code

Code for detecting genomic island insertions in clades of microbes.

Pbxplore ⭐ 17

A suite of tools to explore protein structures with Protein Blocks 🐍

PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.

Open3spn2 ⭐ 16

An implementation of the 3SPN2 and 3SPN2.C coarse-grained DNA forcefields in OpenMM

Deepcoil ⭐ 16

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

Deepfraglib ⭐ 16

Core Genome Alignment ⭐ 16

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

Protein orthologous group assignment with deep learning

Alphaspace2 ⭐ 16

Protein surface topographical mapping tool

Implementation of High Quality Protein Q8 Secondary Structure Prediction by Diverse Neural Network Architectures

Deepdegron ⭐ 16

Deep learning model to predict degron sequences

Metawibele ⭐ 15

MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

Direct coupling analysis software for protein and RNA sequences

DeepDom is an ab-initio method for protein domain boundary prediction

Localcider ⭐ 15

localCIDER - sequence analysis tool for disordered protein sequences

Ampril Genomes ⭐ 15

scripts for the project of seven thaliana genomes assembly

Interfacea ⭐ 15

An open-source library for the analysis of protein interactions.

Dna2proteins ⭐ 15

A Python script to translate DNA sequences to protein sequences

Interpro7 Api ⭐ 15

Siteinterlock ⭐ 15

A novel approach to pose selection in protein-ligand docking based on graph theory.

Set of utilities on sequences and BAM files

Pybindingcurve ⭐ 14

Binding curve simulation and experimental data fitting for multi component protein-ligand systems

Topefind Public ⭐ 14

Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠

Cocoscore ⭐ 14

CoCoScore: context-aware co-occurrence scores for text mining applications

Gcn For Structure And Function ⭐ 14

Code for reproducing results of "Unsupervised embeddings is all you need for protein function prediction"

Dockingml ⭐ 14

A package for MD, Docking and Machine learning drug discovery pipeline

Multiphate ⭐ 14

Throughput PhATE processing of draft or finished phage genomes

Parapred Pytorch ⭐ 14

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

Hypothesis Bio ⭐ 14

Hypothesis extension for computational biology

Bmi219 2017 Proteinfolding ⭐ 14

UCSF BMI219 Deep Learning (2017), Coding example (Prediction of protein folding with RNN and CNN)

Workflow for identifying and classifying homologous gene/protein sequences

Bindpredict ⭐ 14

Prediction of binding residues for metal ions, nucleic acids, and small molecules.

Deepcrystal ⭐ 14

DeepCrystal: A Deep Learning Framework for sequence-based Protein Crystallization Prediction

Dnapacman ⭐ 14

Official implementation of the paper "SAINT"

Proteome-Wide Association Study

Deltavina ⭐ 14

DeltaVina scoring function

Protfeat ⭐ 13

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

Cbh21 Protein Solubility Challenge ⭐ 13

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

Emg Toolkit ⭐ 13

MGnify API toolkit

Progeo Neo ⭐ 13

a Customized Proteogenomic Workflow for Neoantigen Prediction and Selection

Sbm Openmm ⭐ 13

Python library to run structure based model (SBM) simulations using the OpenMM toolkit

volume calculation and segmentation

Improved contact predictions using the recognition of protein like contact patterns.

ResPRE is an algorithm for protein residue-residue contact-map prediction

A tool to infer species tree and phylogenetic network from multilocus data

Pycoevol ⭐ 13

A Python workflow to study protein-protein coevolution and interaction

This is the public repository for the EPIC tool.

Dsol_rv0.2 ⭐ 13

deep protein solubility prediction

Spatiotemporal identification of druggable binding sites using deep learning

Viralrecall ⭐ 12

Detection of NCLDV signatures in 'omic data

A Python tool for parsing and analyzing electron density maps data available from the worldwide Protein Data Bank

Database of Interacting Protein Structures (DIPS)

OMAmer - tree-driven and alignment-free protein assignment to sub-families

Rfscorevs_binary ⭐ 12

RF-Score-VS binary

S2F: protein function without experiments

Cryosparc2_public ⭐ 12

CryoSPARC is the state-of-the-art platform used globally for obtaining 3D structural information from single particle cryo-EM data. The cryoSPARC platform enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.

Sdrf Pipelines ⭐ 12

A repository to convert SDRF proteomics files into pipelines config files

Deepcseqsite ⭐ 12

Protein-ligand binding sites prediction toolkits

A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.

Protein Backbone Strurcture Prediction based on deeplearning

Enlighten2 ⭐ 11

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems

pdbx is a parser module in python for structures of the protein data bank in the mmcif format

Message Passing Neural Network ⭐ 11

Pytorch implementation of a message passing neural network with RNN sub-units

Neural Bacteriocin Identifier - a recurrent neural network based software to predict bacteriocins from protein sequences.

Phagehosts ⭐ 11

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

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