bioinfodlsu/PHIStruct

Published in Bioinformatics. Phage-host interaction prediction tool that incorporates protein structure information in representing receptor-binding proteins (RBPs). It improves performance especially for phages with RBPs that have low sequence similarity to those of known phages

Language: Jupyter Notebook - Size: 15.7 MB - Last synced at: about 22 hours ago - Pushed at: about 23 hours ago - Stars: 4 - Forks: 0

Tracer-Cloud/tracer-client

✨ Real-time monitoring and performance optimization for scientific HPC pipelines on AWS cloud ☁️

Language: Rust - Size: 27.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 7 - Forks: 2

NilsDunlop/PROTACFold

A toolkit developed to predict and analyze PROTAC-mediated protein degradation complexes using AlphaFold3.

Language: Jupyter Notebook - Size: 41.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 18 - Forks: 3

AspirinCode/awesome-BioMolGenFold

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

Size: 189 KB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 30 - Forks: 7

pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

Language: Python - Size: 328 MB - Last synced at: 8 days ago - Pushed at: 13 days ago - Stars: 1,012 - Forks: 76

kyegomez/AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

Language: Python - Size: 2.2 MB - Last synced at: 8 days ago - Pushed at: 10 days ago - Stars: 784 - Forks: 104

shivendrra/enigma2

dna protein prediction using transformer. second version of engima

Language: C - Size: 21.2 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 0

johnnytam100/awesome-protein-design

A curated list of awesome protein design research, software and resources.

Size: 29.3 KB - Last synced at: 6 days ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 1

Not-Chat/ALPHAFOLD3_SERVER

A collection of helpful Python3 Jupyter notebooks for working with the AF3 server. My first repository so please be nice :)

Language: Jupyter Notebook - Size: 98.6 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 3 - Forks: 1

suzuki-2001/adaptyv-protein-comp

Design data and process for the AdaptyvBio protein design competition

Language: Python - Size: 3.55 MB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 10 - Forks: 2

Urinx/alphafold_pytorch

An implementation of the DeepMind's AlphaFold based on PyTorch for research

Language: Python - Size: 19.2 MB - Last synced at: 14 days ago - Pushed at: about 4 years ago - Stars: 395 - Forks: 90

keiran-rowell/Presentations

Group meeting presentations and academic talks

Size: 252 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 0

Kaz-bits/Research-automated-projects

The repository contains all the scripts necessary for the bioinformatic characterisation of the IDRs of Arabidopsis transcription factors.

Language: R - Size: 272 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 2 - Forks: 0

CDDLeiden/PCMol

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

Language: Jupyter Notebook - Size: 4.11 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 63 - Forks: 7

langbnj/alphasync

AlphaSync protein structure processing pipeline

Language: Python - Size: 3.91 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

sami-chaaban/alphascreen

Screen interactions with AlphaFold Multimer

Language: Python - Size: 1.52 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 4

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.

Language: Python - Size: 31.1 MB - Last synced at: 1 day ago - Pushed at: almost 2 years ago - Stars: 70 - Forks: 10

WEHI-ResearchComputing/nf-alphafold

Language: Nextflow - Size: 696 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 3 - Forks: 0

Coda-Research-Group/AlphaFind

AlphaFind: Discover structure similarity across the entire known proteome

Language: TypeScript - Size: 6.75 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 22 - Forks: 2

joelb123/rafm Fork of unmtransinfo/rafm

Reliable AlphaFold Measures

Language: Python - Size: 1.53 MB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

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

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Size: 51.8 KB - Last synced at: 6 days ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 0

wells-wood-research/alphafold2-multiprocessing

Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing

Language: Python - Size: 21.5 KB - Last synced at: 4 days ago - Pushed at: over 3 years ago - Stars: 23 - Forks: 1

brgenzim/Beta

BETA provides datasets of structures and sequences that were not used during AlphaFold training.

Language: Python - Size: 34.2 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Asncodes-80/protein-interaction-networks-graph

Serotonin pathways interaction networks

Language: TeX - Size: 2.08 MB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

srom/afpd

AlphaFold pulldown implementation adapted from https://github.com/KosinskiLab/AlphaPulldown

Language: Jupyter Notebook - Size: 2.52 MB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

boyinthebigcity/AFQuickPlot

Ready-to-go Jupyter notebook for plotting AlphaFold-generated MSAs, per-residue pLDDT, and PAE.

Language: Jupyter Notebook - Size: 2.9 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 1

branchialspace/foldbender

protein graph representation

Language: Python - Size: 190 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1

kuixu/alphafold

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

Language: Python - Size: 5.48 MB - Last synced at: 14 days ago - Pushed at: over 3 years ago - Stars: 101 - Forks: 34

LyonyaZhozhikov/Article-PVP-Study-of-SOPH-script

This article is published in Proteins

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garywei944/FMol

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

Language: Python - Size: 48.1 MB - Last synced at: 16 days ago - Pushed at: over 3 years ago - Stars: 17 - Forks: 2

prehensilecode/alphafold_singularity

Singularity recipe for AlphaFold

Language: Python - Size: 72.3 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 32 - Forks: 12

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

Language: Python - Size: 817 KB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 147 - Forks: 45

EBI-EMBL-Bioinformatics-tools/Bardet-Biedl-Syndrome

BBS Project developed by Ronald Pardo, Ana Sofia Villa and Gabriela Moreno for the course of EBI tools @ Universidad de los Andes 2024-02.

Language: Jupyter Notebook - Size: 10.7 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

mansanlab/alphafoldfetch

A tool for downloading AlphaFold structures using UniProt IDs or FASTA files

Language: Python - Size: 1.94 MB - Last synced at: 17 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 1

dptech-corp/Uni-Fold

An open-source platform for developing protein models beyond AlphaFold.

Language: Python - Size: 8.5 MB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 376 - Forks: 74

jvanheld/intro-bioinfo-L2-SV-AMU-SSV3U15_public

Cours d'introduciton à la bioinformatique, 2ème licence en Sciences de la vie, Aix-Marseille Université (L2 SV AMU)

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huiwenke/MineProt

Stand-alone server for structural proteome curation

Language: PHP - Size: 5.97 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 6 - Forks: 0

ml4bio/Dense-Homolog-Retrieval

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

Language: Python - Size: 26.1 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 40 - Forks: 1

Orpowell/alphafold-analyser

A tool to visualise the results of AlphaFold2 and inspect the quality of structural predictions

Language: Python - Size: 7.06 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 10 - Forks: 4

Alejandro2195/Multiple-File-Protein-prediction-in-AlphaFold2-ColabFold

The provided code snippet forms a critical component of an automated script aimed at facilitating the prediction of protein structures using the AlphaFold model within a Google Colab environment. The script is tailored to handle the simultaneous upload of multiple input files, each containing multiple protein sequences for prediction.

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refresh-bio/protestar

Protein Structure Archiver

Language: C++ - Size: 61.5 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 7 - Forks: 0

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

Language: Python - Size: 35 MB - Last synced at: 8 days ago - Pushed at: 11 months ago - Stars: 4 - Forks: 0

Bio2Byte/public_notebooks

Repository of Jupyter Notebooks created by the Bio2Byte group

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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.

Language: Python - Size: 672 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

Attornado/protein-representation-learning Fork of shionhonda/gae-dgl

Protein representation learning using graph neural networks and Alphafold generated 3D structures.

Language: Python - Size: 1.76 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

rvhonorato/alphafold-hpc-wrapper 📦

AlphaFold-wrapper for small HPC

Language: Go - Size: 43.9 KB - Last synced at: 26 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Rishit-dagli/Invariant-Attention

An implementation of Invariant Point Attention from Alphafold 2

Language: Python - Size: 326 KB - Last synced at: 8 days ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

BiCU-CCRI/ab13_Alphafold_test

Establishing and testing AlphaFold on GPU

Size: 0 Bytes - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MiklosKralik/AlphaDock

Examines ligand interactions with predicted protein structures

Language: Jupyter Notebook - Size: 4.77 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 2

raqmejtru/mitonuclear-sd

Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.

Language: R - Size: 91.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

AlanAloha/hmonster

Prediction of possible paths of gene mutation using AlphaFold

Language: Python - Size: 2.76 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

elttaes/Revisiting-PLMs

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

Language: Python - Size: 6.55 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 41 - Forks: 9

johnnytam100/AlphaCutter

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

Language: Python - Size: 599 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

sami-chaaban/Colabfold

Colabfold setup and scripts

Language: Shell - Size: 43.9 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

hds-sandbox/AlphaFold_Workshop

Predict protein folding structures using ColabFold. Gain a deeper understanding of protein folding prediction with AlphaFold2 and MMseqs2. Run the Jupyter notebook on UCloud, learn to interpret results, predict protein structures of interest. Technical requirements provided. Enhance your knowledge of protein folding and AlphaFold2's principles. Fam

Language: Jupyter Notebook - Size: 567 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/training.alphafold

AlphaFold predictions of protein structure on Sydney Research Compute Infrastructure

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cbalbin-bio/pymol-color-alphafold

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

Language: Python - Size: 1.88 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 33 - Forks: 13

mvictoriabuss/Protein_Structure_Prediction

Repository with scripts and data generated during my internship at Institut Pasteur of Paris

Language: Python - Size: 3.19 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

dhakalnirajan/alphafold Fork of google-deepmind/alphafold

Open source code for AlphaFold.

Language: Python - Size: 15.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

wangleiofficial/FAPEloss

alphafold FAPE loss

Language: Python - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Zuricho/alphafold_wiki

AlphaFold Unofficial Wiki

Language: Jupyter Notebook - Size: 171 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

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).

Language: Shell - Size: 6.84 KB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0