alphafold2

There are 4 repositories under alphafold2 topic.

aqlaboratory / openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
alphafold2 protein-structure pytorch
Language:Python 2511
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 867
FastFold
hpcaitech / FastFold
Optimizing AlphaFold Training and Inference on GPU Clusters
alphafold2 protein-structure pytorch gpu evoformer parallelism protein-folding cuda habana-gaudi
Language:Python 548
baaihealth / OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
alphafold2 protein-structure pytorch rna-structure
Language:Python 242
westlake-repl / SaProt
Saprot: Protein Language Model with Structural Alphabet
alphafold2 foldseek predicted-structures pretraining protein protein-language-model protein-sequence protein-structure representation-learning structure-aware protein-llm structural-alphbet
Language:Python 222
dptech-corp / Uni-Fold-jax
Trainable AlphaFold implementation in JAX
alphafold2 deep-learning jax
Language:Python 154
af2complex
FreshAirTonight / af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
bioinformatics deep-learning alphafold2 protein-complexes protein-protein-interaction protein-structure-prediction protein-protein-docking
Language:Python 138
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 130
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
soedinglab / MMseqs2-App
MMseqs2 app to run on your workstation or servers
sequence-search electron vue golang docker docker-compose profile-search bioinformatics mmseqs foldseek structure-search alphafold2 colabfold
Language:Vue 51
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
FrameDiPT
instadeepai / FrameDiPT
FrameDiPT: an SE(3) diffusion model for protein structure inpainting
alphafold2 diffusion-models inpainting protein-structure tcr generative-model loop-design protein-folding
Language:Jupyter Notebook 44
nf-core / proteinfold
Protein 3D structure prediction pipeline
workflow protein-structure protein-sequences protein-folding protein-fold-prediction alphafold2 pipeline nextflow nf-core
Language:Nextflow 41
lipan6461188 / AlphaFold-StepByStep
Run AlphaFold2 (and multimer) step by step
alphafold2 alphafold-multimer
Language:Python 28
pengzhangzhi / Awesome-Computational-Structural-Biology
A curated list of awesome self-learning materials in Computational Structural Biology, such as sources, tutorials, etc.
alphafold2 awesome awesome-list bioinformatics computational-biology deep-learning deep-neural-networks
27
aws-samples / aws-rosettafold
Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.
rosettafold alphafold2 deep-learning aws aws-batch protein-folding hpc
Language:Python 22
sbhakat / AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
metadynamics molecular-dynamics markov-state-model alphafold2
Language:Jupyter Notebook 21
PROST
ShahidIqb / PROST
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.
alphafold2 missense-mutations protein-sequences protein-structure stability
Language:Python 20
colbyford / SARS-CoV-2_B.1.1.529_Spike-RBD_Predictions
AlphaFold2 and RoseTTAFold predictions of the SARS-CoV-2 B.1.1.529 variant Spike protein with HADDOCK antibody interactions
sars-cov-2 covid-19 alphafold2 haddock deep-learning machine-learning computational-biology bioinformatics antibody rosettafold
Language:Jupyter Notebook 12
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
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
LightMHC
instadeepai / LightMHC
LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
alphafold2 graphneuralnetwork pmhc protein-structure
Language:Python 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
alphafold2 structural-biology structural-bioinformatics alphafold
Language:Python 9
Ojas-Singh / Re-Glyco
The Python software re-glycosylates protein structures using MD simulation results from the glycoshape database. It takes alphafold protein structures as input and outputs modified structures with glycans added at appropriate sites.
alphafold2 glycans glycoprotein glycosylation
Language:Python 7
sb-ncbr / AlphaCharges
𝛂Charges: A tool for the quick calculation of partial atomic charges for protein structures from AlphaFoldDB
alphafold2 partial-atomic-charges protonation
Language:Python 7
fmi-basel / GUIFold
GUI for running jobs with a local installation of AlphaFold2. Supports submission to queuing systems.
alphafold-multimer alphafold2 gui pipeline
Language:Python 6
Rishit-dagli / Invariant-Attention
An implementation of Invariant Point Attention from Alphafold 2
alphafold alphafold2 deep-learning machine-learning attention attention-mechanism transformer tensorflow
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
MishterBluesky / Conservation-Colab
This Google colab notebook, allows for conservation analysis of user input genes, on their local machine. It relies on the MMSeq2 introduced by https://www.nature.com/articles/s41592-022-01488-1
alphafold2 amino-acid-sequence conservation
Language:Jupyter Notebook 5
neftlon / af2-plddt-contextualized
AlphaFold 2's confidence scores put into context
alphafold2 bioinformatics
Language:Jupyter Notebook 5
tuftsdatalab / Intro_To_AlphaFold2
A Tufts Research Technology Workshop detailing how to use AlphaFold 2 on the Tufts HPC cluster
workshop alphafold2 alphafold-multimer protein-structure
Language:HTML 5
adriandavila / drug-binding-site-model
Predicting probable drug-binding sites for thousands of human proteins using AlphaFold2 predicted 3D protein structures.
alphafold2 data-science graph-convolutional-network machine-learning
Language:Jupyter Notebook 4
sb-ncbr / FFFold
FFFold: A tool for the quick optimisation of protein structures from AlphaFold DB
alphafold2 protonation gfn-ff force-field-optimisation protein-structure-optimisation
Language:JavaScript 4
Shall-We-Dance / AlphaFold-DB
Fix Database problem for AlphaFold by updating some databases.
alphafold2 database
Language:Shell 4
gromdimon / AlphaFold_Glycoprotein
Using AlphaFold Artificial Intelligence for prediction Coronavirus glycoprotein structures
alphafold2 deep-learning machine-learning
Language:Jupyter Notebook 3

alphafold2

aqlaboratory / openfold

pachterlab / gget

hpcaitech / FastFold

baaihealth / OpenComplex

westlake-repl / SaProt

dptech-corp / Uni-Fold-jax

FreshAirTonight / af2complex

Zuricho / ParallelFold

elttaes / Revisiting-PLMs

soedinglab / MMseqs2-App

cbalbin-bio / pymol-color-alphafold

instadeepai / FrameDiPT

nf-core / proteinfold

lipan6461188 / AlphaFold-StepByStep

pengzhangzhi / Awesome-Computational-Structural-Biology

aws-samples / aws-rosettafold

sbhakat / AF-cryptic-pocket

ShahidIqb / PROST

colbyford / SARS-CoV-2_B.1.1.529_Spike-RBD_Predictions

johnnytam100 / awesome-protein-design

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

instadeepai / LightMHC

johnnytam100 / AlphaCutter

Orpowell / alphafold-analyser

Ojas-Singh / Re-Glyco

sb-ncbr / AlphaCharges

fmi-basel / GUIFold

Rishit-dagli / Invariant-Attention

branchialspace / foldbender

MishterBluesky / Conservation-Colab

neftlon / af2-plddt-contextualized

tuftsdatalab / Intro_To_AlphaFold2

adriandavila / drug-binding-site-model

sb-ncbr / FFFold

Shall-We-Dance / AlphaFold-DB

gromdimon / AlphaFold_Glycoprotein