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Search results for protein structure
protein-structure
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173 search results found
Biopython
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3,918
Official git repository for Biopython (originally converted from CVS)
Openfold
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2,235
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Graphein
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932
Protein Graph Library
Molecularnodes
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729
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
Biopandas
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673
Working with molecular structures in pandas DataFrames
Proteinnet
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623
Standardized data set for machine learning of protein structure
Biojava
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564
📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.
Foldseek
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545
Foldseek enables fast and sensitive comparisons of large structure sets.
Fastfold
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485
Optimizing AlphaFold Training and Inference on GPU Clusters
Hh Suite
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429
Remote protein homology detection suite.
Bio_embeddings
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357
Get protein embeddings from protein sequences
Tape
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348
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
Molly.jl
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344
Molecular simulation in Julia
Equibind
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321
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
Uni Fold
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320
An open-source platform for developing protein models beyond AlphaFold.
Plip
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320
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
Rgn
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263
Recurrent Geometric Networks for end-to-end differentiable learning of protein structure
Pypdb
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258
A Python API for the RCSB Protein Data Bank (PDB)
Sidechainnet
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256
An all-atom protein structure dataset for machine learning.
Lightdock
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234
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Jupyter_dock
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215
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
Ligan
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206
Deep generative models of 3D grids for structure-based drug discovery
Protein Sequence Embedding Iclr2019
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203
Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
P2rank
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193
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.
Gemmi
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180
macromolecular crystallography library and utilities
Openprotein
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161
A PyTorch framework for prediction of tertiary protein structure
Dspp Keras
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160
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
Stmol
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152
This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
Proteinflow
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151
Versatile computational pipeline for processing protein structure data for deep learning applications.
Awesome Ai Based Protein Design
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146
A collection of research papers for AI-based protein design
Opencomplex
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130
Trainable PyTorch framework for developing protein, RNA and complex models.
Foldcomp
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127
Compressing protein structures effectively with torsion angles
Saprot
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121
Official implementation of SaProt.
Tape Neurips2019
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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
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115
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Seqvec
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112
Modelling the Language of Life - Deep Learning Protein Sequences
Biojava Tutorial
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111
📖📚An introductory tutorial for BioJava
Ssbio
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96
A Python framework for structural systems biology
Proteinsecondarystructure Cnn
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93
Protein Secondary Structure predictor using Convolutional Neural Networks
Proteinworkshop
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93
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities.
Plmc
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83
Inference of couplings in proteins and RNAs from sequence variation
Deepblast
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80
Neural Networks for Protein Sequence Alignment
R3dmol
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78
🧬 An R package for visualizing molecular data in 3D
Biostructures.jl
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77
A Julia package to read, write and manipulate macromolecular structures (particularly proteins)
Awesome Cryoem
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70
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
Mmtf Pyspark
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64
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
Imp
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64
The Integrative Modeling Platform
Pesto
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64
Geometric deep learning method to predict protein binding interfaces from a protein structure.
Mitos.jl
⭐
64
Mutual Information Tools for protein Sequence analysis in Julia
Ddpm Proteins
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64
A denoising diffusion probabilistic model (DDPM) tailored for conditional generation of protein distograms
Pymod
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61
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
Toolkit
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57
The MPI Bioinformatics Toolkit
Vscoding Sequence
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56
VSCode Extension for interactively visualising protein structure data in the editor
Awesome Structural Bioinformatics
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54
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Gym Lattice
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52
An HP 2D Lattice Environment with a Gym-like API for the Protein Folding Problem
Dmpfold
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51
De novo protein structure prediction using iteratively predicted structural constraints
Progres
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47
Fast protein structure searching or your money back
Mmterm
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46
View proteins and trajectories in the terminal
Mmtf
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43
The specification of the MMTF format for biological structures
Deepaccnet
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40
Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.
Hotspot3d
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33
3D hotspot mutation proximity analysis tool
Molearn
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33
protein conformational spaces meet machine learning
Enspara
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32
Modeling molecular ensembles with scalable data structures and parallel computing
Bio3dview.jl
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32
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto
Molart
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31
MOLeculAR structure annoTator
Ramanet
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31
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
Geometric Vector Perceptron
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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
Manyfold
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28
🧬 ManyFold: An efficient and flexible library for training and validating protein folding models
Deepcov
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28
Fully convolutional neural networks for protein residue-residue contact prediction
Packman
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28
PACKMAN: PACKing and Motion ANalysis
Pyhdx
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27
Derive ΔG for single residues from HDX-MS data
Proteinfold
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26
Protein 3D structure prediction pipeline
Mdciao
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26
mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
Protein Vae
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26
Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies
Libcifpp
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26
Library containing code to manipulate mmCIF and PDB files
Mmtf Genomics
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25
Methods for mapping genomic data onto 3D protein structure.
Gcwgan
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25
Guided Conditional Wasserstein GAN for De Novo Protein Design
Protein Transformer
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25
Predicting protein structure through sequence modeling
Parapred
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25
Paratope Prediction using Deep Learning
Pdbcolor
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24
Python code to color a PDB structure based on parameters from a multiple sequence alignment
Framedipt
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24
FrameDiPT: an SE(3) diffusion model for protein structure inpainting
Glycosylator
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23
Framework for the rapid modeling glycans and glycoproteins.
Chem.cr
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22
Library for dealing with computational chemistry files
Biostructmap
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22
A Python package for mapping sequence aligned data onto protein structures
Geometricus
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22
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
Proteinensembles.jl
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21
Generate and perturb protein structural ensembles using the ExProSE algorithm
Pnerf
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21
Lightdock Python2.7
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20
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
Voronota
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20
Voronota is a software tool for analyzing three-dimensional structures of biological macromolecules using the Voronoi diagram of atomic balls.
Getpdb
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20
Download pdb/protein structures from Uniprot id; This script will download related PDB files, extract chains(Optional), remove duplicates(Optional, maybe lost some conformation changed structures) and save as "UniprotID-PDBID-ModelID-ChainID.pdb/cif".
Caretta
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20
A software-suite to perform multiple protein structure alignment and structure feature extraction.
Hpdb
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19
PDB parser in Haskell
Mmtf Spark
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19
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
Cryptosite
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19
Library for prediction of cryptic binding sites
Pytorch Rgn
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19
Recurrent Geometric Network in Pytorch
Metagenomic Deepfri
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19
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
Guides
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18
A new workflow for the custom design of CRISPR libraries.
Michelanglo App
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17
A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site
Prost
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17
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
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16
PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.
1-100 of 173 search results
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