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499 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Corona ⭐ 2,441

Reverse engineering SARS-CoV-2

Graphein ⭐ 932

Protein Graph Library

Molecularnodes ⭐ 729

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Paddlehelix ⭐ 729

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

Proteinnet ⭐ 623

Standardized data set for machine learning of protein structure

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

ProSPr: Protein Structure Prediction

Official release of the ProGen models

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

A Python Package for Protein Dynamics Analysis

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

Equibind ⭐ 321

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Pdb Tools ⭐ 319

A dependency-free cross-platform swiss army knife for PDB files.

Interaction Fingerprints for protein-ligand complexes and more

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

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

Sidechainnet ⭐ 256

An all-atom protein structure dataset for machine learning.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Lightdock ⭐ 234

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

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

A Python frontend to (Open Biomedical) Ontologies.

Protein Sequence Embedding Iclr2019 ⭐ 203

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

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

Moleculekit ⭐ 183

MoleculeKit: Your favorite molecule manipulation kit

Deepfri ⭐ 156

Deep functional residue identification

Deeprank ⭐ 145

This repository has been integrated in https://github.com/DeepRank/deeprank2

UniRep model, usage, and examples.

Network Embedding as Matrix Factorization: Unifying DeepWalk, LINE, PTE, and node2vec

Pecanpy ⭐ 133

A fast, parallelized, memory efficient, and cache-optimized Python implementation of node2vec

Trrosetta ⭐ 131

A package to predict protein inter-residue geometries from sequence data

Official implementation of SaProt.

Mol Instructions ⭐ 116

Mol-Instructions is a Large-Scale Biomolecules Instruction Dataset for Large Language Models.

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)

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

Run_dbcan ⭐ 109

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

Buddysuite ⭐ 105

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Beautiful Atoms ⭐ 102

Python module for drawing and rendering beautiful atoms and molecules using Blender.

Ifeature ⭐ 99

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.

Bioblender ⭐ 98

AddOn for Blender to do molecular work

Chatdrug ⭐ 96

LLM for Drug Editing, ICLR 2024

Thermonet ⭐ 95

ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

Proteinsecondarystructure Cnn ⭐ 93

Protein Secondary Structure predictor using Convolutional Neural Networks

Proteinworkshop ⭐ 93

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities.

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

Transvar ⭐ 91

TransVar - multiway annotator for precision medicine

Protein Ebm ⭐ 81

Energy-based models for atomic-resolution protein conformations

Kaggle_human_protein_baseline ⭐ 81

Human Protein Atlas Image Classification baseline:0.456

Raptorx 3dmodeling ⭐ 81

Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will update this as soon as possible.

Cpi_prediction ⭐ 80

This is a code for compound-protein interaction (CPI) prediction based on a graph neural network (GNN) for compounds and a convolutional neural network (CNN) for proteins.

Deepblast ⭐ 80

Neural Networks for Protein Sequence Alignment

Deepaffinity ⭐ 80

Protein-compound affinity prediction through unified RNN-CNN

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

Haddock3 ⭐ 76

Official repo of the modular BioExcel version of HADDOCK

Protein Science ⭐ 76

A collection of useful tutorials for Protein Science

Predict the binding affinity of protein-protein complexes from structural data

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

A new approach for representing biological sequences

Transformercpi ⭐ 71

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

Opencadd ⭐ 70

A Python library for structural cheminformatics

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Pdbtools ⭐ 68

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Deepnovo ⭐ 67

Protein Identification with Deep Learning

Dfast_core ⭐ 67

DDBJ Fast Annotation and Submission Tool

Awesome Deep Learning 4 Life Sciences ⭐ 65

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

Mmtf Pyspark ⭐ 64

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

Genomes Pipeline ⭐ 63

MGnify genome analysis pipeline

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

Coronavirus_structural_task_force ⭐ 60

Repository for the molecular structures related with Corona virusses and their re-processing

PyGBe: Python, GPUs and Boundary elements for electrostatics

Equifold ⭐ 59

Official code repository for EquiFold

Python Graph Clustering ⭐ 59

A collection of Python scripts that implement various graph clustering algorithms, specifically for identifying protein complexes from protein-protein interaction networks.

The Fluorescent Protein Database

Cytoself ⭐ 58

Self-supervised models for encoding protein localization patterns from microscopy images

Udsmprot ⭐ 58

Protein sequence classification with self-supervised pretraining

This is the repository for PIPR. This repository contains the source code and links to some datasets used in the ISMB/ECCB-2019 paper "Multifaceted Protein-Protein Interaction Prediction Based on Siamese Residual RCNN".

Getcontacts ⭐ 56

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

A tool to identify CLIP-seq peaks

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

Protein Interaction Network ⭐ 53

Computes a molecular graph for protein structures.

Gym Lattice ⭐ 52

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

A Deep-learning based dOcking decoy eValuation mEthod

Raptorx Contact ⭐ 52

Deep residual neural network for protein contact/distance prediction developed by Xu group

Genomegtftools ⭐ 52

convert various features into a GFF-like file for use in genome browsers

Bioinformatics utilities.

Cite Seq Count ⭐ 50

A tool that allows to get UMI counts from a single cell protein assay

A package to annotate protein sequences

retrieve protein sequence identifiers and metadata from http://uniprot.org

Deeprank Gnn ⭐ 48

Graph Network for protein-protein interface

Protein Interface Prediction using Graph Convolutional Networks

Bioblender21 ⭐ 47

Blender plugin to process biological data and molecular work.

Gnn_dove ⭐ 47

Code for "Protein Docking Model Evaluation by Graph Neural Networks"

Proteingcn ⭐ 47

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

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