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Search results for python protein structure

protein-structure x

93 search results found

Biopython ⭐ 3,918

Official git repository for Biopython (originally converted from CVS)

Openfold ⭐ 2,235

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Graphein ⭐ 932

Protein Graph Library

Molecularnodes ⭐ 729

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

Proteinnet ⭐ 623

Standardized data set for machine learning of protein structure

Fastfold ⭐ 485

Optimizing AlphaFold Training and Inference on GPU Clusters

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

Uni Fold ⭐ 320

An open-source platform for developing protein models beyond AlphaFold.

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.

Lightdock ⭐ 234

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

Protein Sequence Embedding Iclr2019 ⭐ 203

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

This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.

Proteinflow ⭐ 151

Versatile computational pipeline for processing protein structure data for deep learning applications.

Opencomplex ⭐ 130

Trainable PyTorch framework for developing protein, RNA and complex models.

Official implementation of SaProt.

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)

Deeplytough ⭐ 115

DeeplyTough: Learning Structural Comparison of Protein Binding Sites

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

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.

Deepblast ⭐ 80

Neural Networks for Protein Sequence Alignment

Ddpm Proteins ⭐ 64

A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms

The Integrative Modeling Platform

Mmtf Pyspark ⭐ 64

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

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

Gym Lattice ⭐ 52

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

Fast protein structure searching or your money back

View proteins and trajectories in the terminal

Deepaccnet ⭐ 40

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

protein conformational spaces meet machine learning

Modeling molecular ensembles with scalable data structures and parallel computing

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

Geometric Vector Perceptron ⭐ 29

Implementation of Geometric Vector Perceptron, a simple circuit for 3d rotation equivariance for learning over large biomolecules, in Pytorch. Idea proposed and accepted at ICLR 2021

Fully convolutional neural networks for protein residue-residue contact prediction

PACKMAN: PACKing and Motion ANalysis

Manyfold ⭐ 28

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

Derive ΔG for single residues from HDX-MS data

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods

Protein Vae ⭐ 26

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

Parapred ⭐ 25

Paratope Prediction using Deep Learning

Pdbcolor ⭐ 24

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

Glycosylator ⭐ 23

Framework for the rapid modeling glycans and glycoproteins.

Biostructmap ⭐ 22

A Python package for mapping sequence aligned data onto protein structures

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

Cryptosite ⭐ 19

Library for prediction of cryptic binding sites

Metagenomic Deepfri ⭐ 19

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

A tool for predicting the effects of missense mutations on protein stability changes upon missense mutation using protein sequence only. PROST uses colab AlhpaFold2 for the prediction of pdb struture from FASTA sequence.

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

Siteinterlock ⭐ 15

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

Jupyterlabpymolpysnips ⭐ 14

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

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.

Ramachandraw ⭐ 12

Ramachandran plotting tool

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

Bib'23: Improved the Heterodimer Protein Complex Prediction with Protein Language Models

Python Modeling Interface

Allopred ⭐ 11

Predict allosteric pockets on proteins

Detects hotspot regions for somatic mutations in 3D protein structures

Equivariant Nn Zoo ⭐ 10

A library for building equivariant neural networks and a zoo of implementations & examples.

Zincbinddb ⭐ 10

The database and API backend for ZincBind - the database of zinc binding sites

2D portraits of 3D protein structures

Cazy_webscraper ⭐ 10

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

A bare metal Python library for building and manipulating protein molecular structures

Farseer Nmr ⭐ 9

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

Easypymol ⭐ 9

Script to facilitate the making of horizontal scripts

Pymissense ⭐ 9

PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.

Vaxdesign ⭐ 9

A script that computationally designs a vaccine

Multi-Atom Structure/Selection Toolkit with Interaction Capabilities

Siteinterlock ⭐ 8

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

MD DaVis: A python package to analyze molecular dynamics trajectories of proteins

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

⚔️Find splicing-led, functional changes of the proteome.

Python_scripts ⭐ 7

scripts for parsing PDB, fasta, and GO

Pdb2uniprot ⭐ 7

Convert PDB residues to their Uniprot equivalents

Exmachina ⭐ 6

Sequence aligner for accurate template-based protein structure prediction

Universal Transforming Geometric Network for protein structure prediction.

Alphacutter ⭐ 6

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

The library to support reading and writing of RMF files.

Scipion Chem ⭐ 6

Base Scipion plugin defining objects and protocols for CHEMoinformatics

Protein-Protein Docking using Genetic Algorithm

Diffmodeler ⭐ 5

DiffModeler: a diffusion model based protein complex structure modeling tool.

Web server for automated modeling of loops in protein structures

Vizsnp St ⭐ 5

Visualizing the effect of SNPs on protein structure using iCn3D

Ps4 Dataset ⭐ 5

The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

Rotamer Interaction Field Python Libraries for Computational Protein Design

Cellscape ⭐ 5

Vector graphics cartoons from protein structure

Protein_pretrain ⭐ 5

Multimodal Pretraining for Unsupervised Protein Representation Learning

Biographs ⭐ 5

Python class to easily deal with protein networks.

a set of classes and submodules to build, manipulate and analyse three-dimensional protein structures.

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