alphafold

There are 9 repositories under alphafold topic.

gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold2 databases enrichment-analysis ensembl gget ncbi reference uniprot alphafold archs4 blast enrichr
Language:Python 868
kyegomez / AlphaFold3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
ai alphafold artificial-intelligence bio biology biology-ai geneml ml
Language:Python 572
Urinx / alphafold_pytorch
An implementation of the DeepMind's AlphaFold based on PyTorch for research
alphafold protein-structure-prediction contact-prediction deep-learning pytorch-implementation casp13 structure-prediction
Language:Python 384
Uni-Fold
dptech-corp / Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
alphafold alphafold-multimer protein-structure deep-learning pytorch
Language:Python 349
Zuricho / ParallelFold
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
alphafold alphafold2 parafold parallelization
Language:Python 131
kuixu / alphafold
Install alphafold on the local machine, get out of docker.
alphafold
Language:Python 97
twoXes / awesome-structural-bioinformatics
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.
molecular-informatics chemistry machine-learning deep-learning cheminformatics biology quantum-chemistry docking protein alphafold protein-structure-prediction awesome-list bioinformatics bioinformatics-pipeline bioinformatics-analysis proteomics genomics genetics genome-alignment protein-structure
Language:Python 56
elttaes / Revisiting-PLMs
Exploring Evolution-aware & free protein language models as protein function predictors
alphafold function-prediction fitness-prediction alphafold2 benchmark contact-prediction multiple-sequence-alignment protein-annotation protein-classification protein-language-model pytorch stability esm1b metal-ion-binding msa-construction msa-transformer remote-homology-detection zero-shot-prediction
Language:Python 55
cbalbin-bio / pymol-color-alphafold
PyMOL extension to color AlphaFold structures by confidence (pLDDT).
alphafold alphafold2 bioinformatics computational-biology protein-structure structural-biology pymol pymol-plugin
Language:Python 49
CDDLeiden / PCMol
Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.
alphafold drug-discovery proteochemometrics de-novo-drug-design cheminformatics protein-language-models
Language:Python 35
prehensilecode / alphafold_singularity
Singularity recipe for AlphaFold
alphafold singularity hpc protein-folding containers containerization high-performance-computing slurm apptainer
Language:Python 30
wells-wood-research / alphafold2-multiprocessing
Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing
alphafold multiprocessing
Language:Python 22
garywei944 / FMol
A simplified drug discovery pipeline -- generating SMILE molecular with AlphaSMILES, predicting protein structure with AlphaFold, and checking the druggability with fpocket/Amber.
protein alphafold fpocket drug-discovery
Language:Python 15
Coda-Research-Group / AlphaFind
AlphaFind: Discover structure similarity across the entire known proteome
alphafold lmi proteins structural-similarity alphafind
Language:TypeScript 14
johnnytam100 / awesome-protein-design
A curated list of awesome protein design research, software and resources.
alphafold alphafold-multimer alphafold2 bioinformatics bioinformatics-tool molecular-biology protein-design protein-function protein-sequence protein-structure structural-bioinformatics structural-biology protein-engineering protein-folding protein-protein-interaction protein-structure-prediction
11
AspirinCode / awesome-BioMolFold
RNA, mRNA, DNA, Peptide, Protein, Antibody and Complex | Folding
alphafold alphafold-multimer esmfold openfold rosettafold equifold omegafold uni-fold
10
wudangt / awesome-molecular-modeling-and-drug-discovery
A curated list of awesome Molecular Modeling And Drug Discovery 🔥
molecular-modeling alphafold alphafold2 bioinformatics drug-discovery protein-engineering protein-sequence protein-structure structural-biology molecular-docking molecular-evolution molecular-generation
10
public_notebooks
Bio2Byte / public_notebooks
Repository of Jupyter Notebooks created by the Bio2Byte group
bioinformatics proteins alphafold dynamine agmata disomine efoldmine biology bioinformatics-data jupyter-notebook
Language:Jupyter Notebook 9
johnnytam100 / AlphaCutter
This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.
alphafold alphafold-multimer alphafold2 alphafold3 bioinformatics disordered-proteins protein protein-structure structure
Language:Python 9
Orpowell / alphafold-analyser
A tool to visualise the results of AlphaFold2 and inspect the quality of structural predictions
alphafold alphafold2 structural-bioinformatics structural-biology
Language:Python 9
refresh-bio / protestar
Protein Structure Archiver
alphafold compression mmcif pdb proteins
Language:C++ 7
Rishit-dagli / Invariant-Attention
An implementation of Invariant Point Attention from Alphafold 2
alphafold alphafold2 attention attention-mechanism deep-learning machine-learning tensorflow transformer
Language:Python 6
sami-chaaban / alphascreen
Screen interactions with AlphaFold-Multimer
alphafold protein-protein-interaction alphafold-multimer
Language:Python 6
branchialspace / foldbender
molecular graph representation
alphafold alphafold2 networkx protein-function-prediction pytorch-geometric bioinformatics cafa gene-ontology kaggle pdb dssp
Language:Python 5
huiwenke / MineProt
Stand-alone server for structural proteome curation
alphafold protein server colabfold protein-structure
Language:PHP 5
AlphaDock
MiklosKralik / AlphaDock
Examines ligand interactions with predicted protein structures
structural biology alphafold open-babel autodock vina
Language:Jupyter Notebook 5
Charmve / AlphaFold-baseline
This package provides an basic implementation of the contact prediction network used in AlphaFold 1 for beginner, associated model weights and CASP13 dataset as used for CASP13 (2018) and published in Nature
alphafold baseline protein-protein-interaction protein-structure
Language:Python 4
wangleiofficial / FAPEloss
alphafold FAPE loss
pytorch-implementation alphafold fape
Language:Python 4
Attornado / protein-representation-learning
Protein representation learning using graph neural networks and Alphafold generated 3D structures.
alphafold gnn graph-neural-network protein-structure alphafo
Language:Python 3
jhrcook / proof-of-concept-alphafold
A proof-of-concept for using AlphaFold with new amino acid sequences (this may change to a full project in the future).
alphafold python3 tensorflow jupyterlab bioinformatics protein-folding
Language:Shell 2
sami-chaaban / Colabfold
Colabfold setup and scripts
alphafold slurm
Language:Shell 2
eliyanovva / project-protein-fold
This repo contains a random forest, a convolutional neural network, and a graph convolutional neural network which predict the binding interaction between olfactory proteins and various chemicals using Alphafold predicted structural data.
neural-network python pytorch tensorflow alphafold
Language:Python 1
rafm
joelb123 / rafm
Reliable AlphaFold Measures
bioinformatics structural-biology pharmacology data-science alphafold protein-structure protein-sequences
Language:Python 1
mvictoriabuss / Protein_Structure_Prediction
Repository with scripts and data generated during my internship at Institut Pasteur of Paris
alphafold2 metagenomics microbiota protein-structure-prediction alphafold
Language:Python 1
rvhonorato / alphafold-hpc-wrapper
AlphaFold-wrapper for small HPC
alphafold alphafold-multimer cli golang hpc slurm wrapper
Language:Go 1
Asncodes-80 / protein-interaction-networks-graph
Serotonin pathways interaction networks
alphafold networkx proteins python
Language:TeX 0

alphafold

pachterlab / gget

kyegomez / AlphaFold3

Urinx / alphafold_pytorch

dptech-corp / Uni-Fold

Zuricho / ParallelFold

kuixu / alphafold

twoXes / awesome-structural-bioinformatics

elttaes / Revisiting-PLMs

cbalbin-bio / pymol-color-alphafold

CDDLeiden / PCMol

prehensilecode / alphafold_singularity

wells-wood-research / alphafold2-multiprocessing

garywei944 / FMol

Coda-Research-Group / AlphaFind

johnnytam100 / awesome-protein-design

AspirinCode / awesome-BioMolFold

wudangt / awesome-molecular-modeling-and-drug-discovery

Bio2Byte / public_notebooks

johnnytam100 / AlphaCutter

Orpowell / alphafold-analyser

refresh-bio / protestar

Rishit-dagli / Invariant-Attention

sami-chaaban / alphascreen

branchialspace / foldbender

huiwenke / MineProt

MiklosKralik / AlphaDock

Charmve / AlphaFold-baseline

wangleiofficial / FAPEloss

Attornado / protein-representation-learning

jhrcook / proof-of-concept-alphafold

sami-chaaban / Colabfold

eliyanovva / project-protein-fold

joelb123 / rafm

mvictoriabuss / Protein_Structure_Prediction

rvhonorato / alphafold-hpc-wrapper

Asncodes-80 / protein-interaction-networks-graph