GitHub topics: protein-folding

Repositories

pram84/rna-3d-folding

🧪Predicting 🧬RNA 3D Structures 🚀ML

Language: Jupyter Notebook - Size: 18.6 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0

lucidrains/triangle-multiplicative-module

Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or columns of a 2d feature map, as a standalone package for Pytorch

Language: Python - Size: 51.8 KB - Last synced at: 2 days ago - Pushed at: almost 4 years ago - Stars: 30 - Forks: 2

MurrellGroup/PyBoltz.jl

Julia bindings for Boltz-1

Language: Julia - Size: 297 KB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

lucidrains/alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

Language: Python - Size: 19.3 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 1,604 - Forks: 264

Joshua-Pillai/TREM2_Variants

TREM2: Variants of Unknown Significance

Language: Python - Size: 5.34 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

Prospr is a universal toolbox for protein structure prediction within the HP-model. The Python package is based on a C++ core, which gives Prospr its high performance. The C++ core is made available as a separate zip file to facilitate high-performance computing applications. The package comes with many prediction algorithms and datasets to use.

Language: C++ - Size: 6.66 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 17 - Forks: 1

hpcaitech/FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters

Language: Python - Size: 1.26 MB - Last synced at: 12 days ago - Pushed at: 11 months ago - Stars: 603 - Forks: 90

PaddlePaddle/PaddleHelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

Language: Python - Size: 131 MB - Last synced at: 13 days ago - Pushed at: 7 months ago - Stars: 1,064 - Forks: 229

krishnaura45/rna-3d-folding

🧪Predicting 🧬RNA 3D Structures 🚀ML

Language: Jupyter Notebook - Size: 19.5 KB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 0

lucidrains/equiformer-pytorch

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

Language: Python - Size: 17.5 MB - Last synced at: 14 days ago - Pushed at: 6 months ago - Stars: 269 - Forks: 27

RosettaCommons/PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Language: Jupyter Notebook - Size: 353 MB - Last synced at: 13 days ago - Pushed at: 10 months ago - Stars: 568 - Forks: 160

lucidrains/invariant-point-attention

Implementation of Invariant Point Attention, used for coordinate refinement in the structure module of Alphafold2, as a standalone Pytorch module

Language: Python - Size: 289 KB - Last synced at: 17 days ago - Pushed at: over 2 years ago - Stars: 163 - Forks: 12

lucidrains/tr-rosetta-pytorch

Implementation of trRosetta and trDesign for Pytorch, made into a convenient package, for protein structure prediction and design

Language: Python - Size: 80.6 MB - Last synced at: 21 days ago - Pushed at: almost 4 years ago - Stars: 82 - Forks: 10

nf-core/proteinfold

Protein 3D structure prediction pipeline

Language: Nextflow - Size: 8.26 MB - Last synced at: about 9 hours ago - Pushed at: about 15 hours ago - Stars: 80 - Forks: 57

mckeownish/Wiggle

Python library for implementing geometrical representations of curves.

Language: Python - Size: 347 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

Iswoon/Protein-folding-tool-JAVA

An interactive and educational tool designed to help middle school students understand the basics of protein folding, mutations, refolding, and denaturation. This fun, visual application uses Java and Swing to simulate the complex process of protein structure formation and changes.

Language: Java - Size: 16.6 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

mpckkk/Python

Play_With_Python

Language: Jupyter Notebook - Size: 150 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

torchmd/torchmd-cg

Example to fit parameters and run CG simulations using TorchMD and Schnet

Language: Jupyter Notebook - Size: 2.64 MB - Last synced at: 10 days ago - Pushed at: over 3 years ago - Stars: 45 - Forks: 11

berylgithub/HP-Protein

Language: Jupyter Notebook - Size: 1020 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

MHosseinHashemi/IASBS_Bioinformatics_Course

Bioinformatics Course Material (Assignments, Final Project, etc)

Language: Jupyter Notebook - Size: 7.72 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

pyDock/AlphaFold3-Conda-Install

Step-by-step guide to install and configure AlphaFold 3 using a Conda Python 3.11 environment. No system-wide installations required. ✅ Miniconda setup & dependencies ✅ Repository cloning & model setup ✅ Database configuration & execution script 🔹 Requirements: Linux, NVIDIA GPU (Ampere+), CUDA, ~700GB disk space.

Language: Shell - Size: 113 KB - Last synced at: 2 months ago - Pushed at: 2 months 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: 26 days ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 1

floriangisperg/jasco_app

A streamlit app extending the capabilities of the Jasco spectra manager for fluorescence-spectroscopy protein analytics

Language: Python - Size: 105 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

instadeepai/manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

Language: Python - Size: 1.39 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 80 - Forks: 9

SPC-Facility-EMBL-Hamburg/circularDichroismApp

R shiny app to analyse circular dichroism data

Language: Python - Size: 16.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 2 - Forks: 1

vvoelz/HPSandbox

a package of Python modules and example scripts for experimenting with the two-dimensional HP lattice model of Dill and Chan.

Language: Python - Size: 76.7 MB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 3

instadeepai/FrameDiPT

FrameDiPT: an SE(3) diffusion model for protein structure inpainting

Language: Jupyter Notebook - Size: 42.4 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 52 - Forks: 6

omarperacha/ps4-dataset

The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.

Language: Python - Size: 4.4 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

renatawong/quantum-protein-structure-prediction

Quantum algorithms for protein structure prediction. Language: Python (Qiskit). Platform: IBM Quantum's backends and simulators.

Language: Jupyter Notebook - Size: 2.37 MB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 7 - Forks: 2

adamkurth/scripts

A home for research related scripts

Language: Shell - Size: 38.1 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

ahabegger/QuantumHoneycombPSP

QuantumHoneycombPSP is a Python-based project designed to model protein structure prediction (PSP) using D-Wave quantum annealing. Uses novel protein lattices and energy functions.

Language: Python - Size: 274 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

prehensilecode/alphafold_singularity

Singularity recipe for AlphaFold

Language: Python - Size: 72.3 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 32 - Forks: 12

bigict/tcr_pmhc

Predicting neoantigen and T-cell receptor binding by integrating structural context and sequence evolutionary conservation

Language: Python - Size: 49.7 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

AstraBert/proteinviz

Your open-source alternative to AlphaFold3🚀

Language: Python - Size: 10.1 MB - Last synced at: 9 days ago - Pushed at: 12 months ago - Stars: 10 - Forks: 0

sialock/protein-folding-

Python code for simulating protein folding using Monte Carlo and analyzing the structure with MDTraj and Bio.PDB

Size: 8.79 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

conradry/prtm

Deep learning for protein science

Language: Python - Size: 909 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 18 - Forks: 1

alec-loftus/Peptide_Folding_Classifier

We seek a classifier that will predict if a protein sequence (+3D coordinates) will fold.

Language: Python - Size: 12 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 3

aws-samples/aws-rosettafold

Infrastructure template and Jupyter notebooks for running RoseTTAFold on AWS Batch.

Language: Python - Size: 26 MB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 22 - Forks: 2

pfwscn/pfwscn.github.io

Summary of my work to model protein folding as graph (SCN) formation

Language: HTML - Size: 18.2 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

dav0dea/protein-folding

Protein structure prediction using optimization methods from the field of machine learning

Language: Jupyter Notebook - Size: 1.28 MB - Last synced at: 10 days ago - Pushed at: almost 3 years ago - Stars: 10 - Forks: 3

AntoinePassemiers/GDE-GaussFold

Lightning-Fast Template-free Protein Folding based on Predicted Residue Contacts and Secondary Structure

Language: Python - Size: 592 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0

ammar-s847/Cyclica-Classification-Challenge

Classifying protein binding sites from the Cyclica dataset. Built for the CxC 2023 Datathon

Language: Jupyter Notebook - Size: 55.2 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ahabegger/CA-2-HCOMB

CA-2-HCOMB is a tool for simplifying single-chain protein structures from PDB files into manageable models like various honeycombs, retaining essential information for in-depth computations. It's efficient for large datasets and machine learning, and user-friendly for research and education.

Language: Python - Size: 2.12 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

jessekommandeur/Protein-Folding

Exploring Uniform Random Sampling in HP Model Protein Folding

Language: Jupyter Notebook - Size: 49.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Fabio-Gil-Z/AlphaMod

AlphaMod's official repository for protein folding

Language: Python - Size: 2.31 GB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

TommyGiak/HP_model

Implementation of the HP protein folding model with commands line interface

Language: Python - Size: 10.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

sarisabban/RosettaAbinitio 📦

A bash script for an automated Rosetta Abinitio folding simulation on an HPC

Language: Shell - Size: 37.1 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 11 - Forks: 6

AndersJing/ResNetQA

ResNetQA: Improved protein model quality assessment by integrating sequential and pairwise features using deep learning

Language: Python - Size: 117 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 2

lorenzoditucci/sda_examples_aws

Examples for SDAccel 2017.1+ on AWS F1 instances

Language: C++ - Size: 29.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 8 years ago - Stars: 6 - Forks: 0

mmui/fiddle Fork of q10/fiddle

Language: Python - Size: 516 KB - Last synced at: almost 2 years ago - Pushed at: almost 14 years ago - Stars: 0 - Forks: 0

BioKT/MasterMSM

Python package for generating Markov state models

Language: Python - Size: 33.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 17 - Forks: 8

thuxugang/opus_fold3

OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow

Language: Python - Size: 65.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

codingPineAppl3/proteinfolding

- The goal was to calculate the maximum possible energy that emerges during protein folding after each generation - I used Genetic Algorithm and Java to do the project

Language: Java - Size: 104 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

thuxugang/opus_fold

OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling

Size: 9.26 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 19 - Forks: 3

3D-Circle/in-fold-we-trust 📦

CTB project

Language: JavaScript - Size: 1.28 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

Related Keywords

protein-folding 67 protein-structure 14 bioinformatics 13 protein-structure-prediction 12 deep-learning 11 python 7 alphafold2 7 artificial-intelligence 7 machine-learning 6 protein-design 5 protein 4 pytorch 3 protein-dynamics 3 protein-docking 3 structure-prediction 3 hpc 3 alphafold 3 structural-biology 3 genetic-algorithm 3 alphafold3 3 rna-structure-prediction 2 protein-sequence 2 jupyter-notebook 2 rosetta 2 simulation 2 protein-secondary-structure 2 aws 2 protein-fold-prediction 2 protein-sequences 2 reinforcement-learning 2 monte-carlo-simulation 2 casp16 2 stanford-machine-learning 2 vfold 2 rna-sequencing 2 high-performance-computing 2 kaggle-competition 2 biology 2 rna-3d-structure 2 research-project 2 quantum-computing 2 simplification 1 backtracking 1 break-sampling 1 containers 1 solution-space-sampling 1 containerization 1 neural-network 1 uniform-random-sampling 1 modeller 1 annealing 1 hp-model 1 pyhton 1 ab-initio 1 job-scheduler 1 protein-potential-functions 1 biotechnology 1 biotech 1 drug-discovery 1 protein-science 1 biopython 1 open-source 1 huggingface-spaces 1 aws-batch 1 rosettafold 1 ai 1 gradient-descent 1 minimization 1 slurm 1 graph-distance 1 singularity 1 l-bfgs 1 protein-3d-structure 1 template-free-modelling 1 classification 1 lattice-model 1 protein-data-bank 1 protein-scoring-functions 1 protein-side-chain-modeling 1 protein-strucutre-prediction 1 protein-torsion-angles 1 fold 1 game 1 stochastic-optimization 1 abinitio-simulations 1 protein-modeling 1 analyses 1 differential-geometry 1 protein-backbones 1 clustering-algorithm 1 r 1 deep-reinforcement-learning 1 jupyterlab 1 python3 1 tensorflow 1 gromacs 1 md-analysis 1 md-simulations 1 structure-based-model 1 monte-carlo 1