alphafold

Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures

parallelization alphafold alphafold2 parafold

UpdatedFeb 25, 2024
Python

ml4bio /Dense-Homolog-Retrieval

Star101

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

protein homology-search protein-structure-prediction alphafold dense-retrieval protein-language-model msa-construction

UpdatedAug 30, 2024
Python

kuixu /alphafold

Star101

Install alphafold on the local machine, get out of docker.

alphafold

UpdatedNov 17, 2021
Python

cbalbin-bio /pymol-color-alphafold

Star88

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

bioinformatics structural-biology pymol-plugin protein-structure computational-biology pymol alphafold alphafold2

UpdatedJul 23, 2024
Python

twoXes /awesome-structural-bioinformatics

Star70

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.

machine-learning bioinformatics deep-learning genomics chemistry genetics cheminformatics biology protein-structure protein bioinformatics-pipeline quantum-chemistry awesome-list proteomics docking bioinformatics-analysis protein-structure-prediction genome-alignment alphafold molecular-informatics

UpdatedMay 5, 2023
Python

elttaes /Revisiting-PLMs

Star63

Exploring Evolution-aware & free protein language models as protein function predictors

benchmark pytorch contact-prediction stability multiple-sequence-alignment protein-annotation function-prediction protein-classification alphafold protein-language-model alphafold2 fitness-prediction zero-shot-prediction msa-construction msa-transformer esm1b remote-homology-detection metal-ion-binding

UpdatedSep 28, 2024
Python

CDDLeiden /PCMol

Star63

Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.

cheminformatics drug-discovery alphafold de-novo-drug-design proteochemometrics chemical-language-models protein-language-models

UpdatedMar 20, 2025
Jupyter Notebook

prehensilecode /alphafold_singularity

Star34

Singularity recipe for AlphaFold

hpc containers slurm singularity high-performance-computing containerization protein-folding alphafold apptainer

UpdatedNov 12, 2024
Python

AspirinCode /awesome-BioMolGenFold

Star28

RNA, mRNA, DNA, Peptide, Protein, Antibody and Complex | Folding

alphafold alphafold-multimer rosettafold openfold esmfold uni-fold omegafold equifold

UpdatedMar 4, 2025

wells-wood-research /alphafold2-multiprocessing

Star23

Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing

multiprocessing alphafold

UpdatedAug 5, 2021
Python

Coda-Research-Group /AlphaFind

Star22

AlphaFind: Discover structure similarity across the entire known proteome

proteins lmi structural-similarity alphafold alphafind

UpdatedFeb 1, 2025
TypeScript

garywei944 /FMol

Star17

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

protein drug-discovery alphafold fpocket