alphafold2

There are 5 repositories under alphafold2 topic.

aqlaboratory / openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
alphafold2 protein-structure pytorch
Language:Python 3111
gget
pachterlab / gget
🧬 gget enables efficient querying of genomic reference databases
alphafold2 databases enrichment-analysis ensembl gget ncbi reference uniprot alphafold archs4 blast enrichr genomics proteomics rna-seq transcriptomics
Language:Python 1055
martinpacesa / BindCraft
User friendly and accurate binder design pipeline
alphafold2 binder design protein pyrosetta
Language:Python 772
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 610
westlake-repl / SaProt
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
alphafold2 foldseek predicted-structures pretraining protein protein-language-model protein-sequence protein-structure representation-learning structure-aware protein-llm structural-alphbet
Language:Python 431
OpenComplex
baaihealth / OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
alphafold2 protein-structure pytorch rna-structure
Language:Python 254
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 164
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 163
dptech-corp / Uni-Fold-jax
Trainable AlphaFold implementation in JAX
alphafold2 deep-learning jax
Language:Python 159
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 96
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 91
nf-core / proteinfold
Protein 3D structure prediction pipeline
workflow protein-structure protein-sequences protein-folding protein-fold-prediction alphafold2 pipeline nextflow nf-core colabfold esmfold
Language:Nextflow 86
elttaes / Revisiting-PLMs
Exploring Evolution-aware & free protein language models as protein function predictors
alphafold alphafold2 benchmark contact-prediction esm1b fitness-prediction function-prediction metal-ion-binding msa-construction msa-transformer multiple-sequence-alignment protein-annotation protein-classification protein-language-model pytorch remote-homology-detection stability zero-shot-prediction
Language:Python 64
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 56
flyark / AFM-LIS
Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)
alphafold-multimer protein-protein-interaction-prediction alphafold2 alphafold3 colabfold
Language:Jupyter Notebook 53
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
42
lipan6461188 / AlphaFold-StepByStep
Run AlphaFold2 (and multimer) step by step
alphafold2 alphafold-multimer
Language:Python 35
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 23
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 22
johnnytam100 / AlphaCutter
This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.
alphafold alphafold-multimer alphafold2 bioinformatics disordered-proteins protein protein-structure structure alphafold3
Language:Python 15
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
14
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 13
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
LightMHC
instadeepai / LightMHC
LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
alphafold2 graphneuralnetwork pmhc protein-structure
Language:Python 12
sb-ncbr / AlphaCharges
𝛂Charges: A tool for the quick calculation of partial atomic charges for protein structures from AlphaFold DB
alphafold2 partial-atomic-charges protonation
Language:Python 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
11
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 10
THU-ATOM / AIRFold
AIRFold Protein Structure Prediction System
alphafold2 esmfold omegafold protein-structure-prediction airfold
Language:Python 10
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 7
neftlon / af2-plddt-contextualized
AlphaFold 2's confidence scores put into context
alphafold2 bioinformatics
Language:Jupyter Notebook 7
branchialspace / foldbender
protein graph representation
alphafold alphafold2 networkx protein-function-prediction pytorch-geometric bioinformatics cafa gene-ontology kaggle pdb dssp
Language:Python 6
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 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
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 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

alphafold2

aqlaboratory / openfold

pachterlab / gget

martinpacesa / BindCraft

hpcaitech / FastFold

westlake-repl / SaProt

baaihealth / OpenComplex

Zuricho / ParallelFold

FreshAirTonight / af2complex

dptech-corp / Uni-Fold-jax

soedinglab / MMseqs2-App

cbalbin-bio / pymol-color-alphafold

nf-core / proteinfold

elttaes / Revisiting-PLMs

instadeepai / FrameDiPT

flyark / AFM-LIS

pengzhangzhi / Awesome-Computational-Structural-Biology

lipan6461188 / AlphaFold-StepByStep

ShahidIqb / PROST

aws-samples / aws-rosettafold

sbhakat / AF-cryptic-pocket

johnnytam100 / AlphaCutter

johnnytam100 / awesome-protein-design

Orpowell / alphafold-analyser

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

instadeepai / LightMHC

sb-ncbr / AlphaCharges

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

Ojas-Singh / Re-Glyco

THU-ATOM / AIRFold

fmi-basel / GUIFold

neftlon / af2-plddt-contextualized

branchialspace / foldbender

MishterBluesky / Conservation-Colab

Rishit-dagli / Invariant-Attention

sb-ncbr / FFFold

tuftsdatalab / Intro_To_AlphaFold2