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: 1.68 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 0

WeeYeZhi/master_logbook_web_app

This is the digital version of my master project's logbook that is created by using Streamlit Python package to document all the command lines and codes that I ran to do my project so that other researchers can later reproduce the exact same analysis results

Language: Python - Size: 489 KB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0

Graylab/DL4Proteins-notebooks

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Language: Jupyter Notebook - Size: 23.4 MB - Last synced at: 16 days ago - Pushed at: 5 months ago - Stars: 415 - Forks: 62

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: 134 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1,079 - Forks: 231

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: 177 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 14 - Forks: 3

urban233/PySSA

Python rich client for visual protein Sequence to Structure Analysis

Language: Python - Size: 336 MB - Last synced at: 1 day ago - Pushed at: 18 days ago - Stars: 18 - Forks: 2

aqlaboratory/rgn

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

Language: Python - Size: 34.7 MB - Last synced at: 9 days ago - Pushed at: about 6 years ago - Stars: 326 - Forks: 87

danielathome19/ProteiNN-Structure-Predictor

A transformer network trained to predict end-to-end single sequence protein structure as a set of angles given amino acid sequences.

Language: Python - Size: 12.5 MB - Last synced at: 2 days ago - Pushed at: 6 months ago - Stars: 6 - Forks: 1

delveopers/Biosaic

KMer level tokenizer for DNA & Proteins sequences

Language: Python - Size: 9.07 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

zjunlp/OntoProtein

[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding

Language: Python - Size: 650 KB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 150 - Forks: 21

amckenna41/protPy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

Language: Python - Size: 255 KB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 0

NilsDunlop/PROTACFold

A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.

Language: Python - Size: 64.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 23 - 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: 7 days ago - Pushed at: over 2 years ago - Stars: 72 - Forks: 10

lucidrains/alphafold3-pytorch

Implementation of Alphafold 3 from Google Deepmind in Pytorch

Language: Python - Size: 13.6 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1,469 - Forks: 189

adenger/subpred_dl

Code for the manuscript "Application of Protein Structure Encodings and Sequence Embeddings for Transporter Substrate Prediction".

Language: Jupyter Notebook - Size: 21.4 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

Eryk96/NetSurfP-3.0

NetSurfP 3.0: Protein secondary structure and relative solvent accessibility prediction

Language: Jupyter Notebook - Size: 37.5 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 21 - Forks: 7

dhanyashri-g/long-covid-therapeutics

A project exploring G-protein-coupled receptors (GPCRs) as therapeutic targets for Long COVID using computational analysis and drug repurposing tools.

Size: 23.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

DeepFoldProtein/DeepFold

Framework for project DeepFold.

Language: Python - Size: 16 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

okkevaneck/prospr

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: 6.67 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 17 - Forks: 1

PrayagParmar77/biosiac

KMer level tokenizer for DNA & Proteins sequences

Size: 7.81 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

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: 4 months ago - Pushed at: about 1 year ago - Stars: 568 - Forks: 160

FreshAirTonight/af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

Language: Python - Size: 4.38 MB - Last synced at: 4 months ago - Pushed at: 12 months ago - Stars: 160 - Forks: 19

taneishi/CB513_dataset

CB513 datasets for Protein Secondary Structure Prediction

Language: Python - Size: 8.61 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 10 - Forks: 1

johnnytam100/awesome-protein-design

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

Size: 29.3 KB - Last synced at: 4 days ago - Pushed at: over 3 years ago - Stars: 14 - Forks: 1

Urinx/alphafold_pytorch

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

Language: Python - Size: 19.2 MB - Last synced at: 4 months ago - Pushed at: over 4 years ago - Stars: 395 - Forks: 90

THU-ATOM/AIRFold

AIRFold Protein Structure Prediction System

Language: Python - Size: 114 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 9 - Forks: 0

SubhangiSati/QuantumFold-Hybrid-Deep-Learning-for-Protein-Structure-Prediction

QuantumFold integrates quantum circuits with classical deep learning to predict protein structures. Utilizing SidechainNet, it combines quantum feature encoding with LSTM layers for accurate predictions. The project offers metric logging, data visualization, and a saved model for advanced protein folding analysis.

Language: Python - Size: 8.75 MB - Last synced at: 4 months ago - Pushed at: 8 months ago - Stars: 4 - Forks: 0

imbforge/fold2go

fold2go is a nextflow pipeline for in silico prediction of protein structures and interactions through various machine learning models.

Language: Python - Size: 705 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

MPI-Dortmund/pymissense

PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.

Language: Python - Size: 1.03 MB - Last synced at: 7 days ago - Pushed at: almost 2 years ago - Stars: 23 - Forks: 0

dohlee/deepab-pytorch

An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.

Language: Python - Size: 15.8 MB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

psipred/DMPfold2

Fast and accurate protein structure prediction

Language: Python - Size: 128 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 49 - Forks: 12

giovancombo/ProteinSecondaryStructurePrediction

A repo containing all the material for the examination exercise from the 2023 Deep Learning course, held by Professor Paolo Frasconi, at the University of Florence, Italy. The exercise focuses on using a Transformer architecture for Protein Secundary Structure Prediction on the CullPDB dataset.

Language: Python - Size: 6.82 MB - Last synced at: 3 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

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: 2 days ago - Pushed at: 11 months ago - Stars: 7 - Forks: 2

dohlee/rosettafold-pytorch

An unofficial re-implementation of RoseTTAFold, a three-track deep learning model for protein structure prediction.

Language: Python - Size: 483 KB - Last synced at: 3 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 2

Bhattacharya-Lab/CASP15

CASP15 performance benchmarking of the state-of-the-art protein structure prediction methods

Size: 88.9 MB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 0

honig-lab/ZEPPI

A method designed for proteome-scale sequence-based evaluation of protein-protein interfaces as defined by structural models of protein-protein interaction complexes.

Language: Python - Size: 4.11 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 2

SAMY-ER/Protein-Structure-Prediction

This project aims to solve a simplified version of the Protein Structure Prediction problem, represented as a combinatorial optimization task, using Reinforcement Learning.

Language: Python - Size: 12 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 4

Praetorius-Lab/.github

Praetorius Lab for Biomolecular Design

Size: 2.93 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

zhukovanadezhda/protein-threading

⚛️📈Protein threading implementation using double dynamic programming👥💻

Language: Python - Size: 1.98 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

dohlee/igfold-pytorch

Unofficial re-implementation of IgFold, a fast antibody structure prediction method, in PyTorch.

Language: Python - Size: 258 KB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

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: about 1 year ago - Pushed at: about 1 year ago - Stars: 40 - Forks: 1

psipred/DMPfold

De novo protein structure prediction using iteratively predicted structural constraints

Language: C - Size: 195 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 55 - Forks: 16

CompSoftMatterBiophysics-CityU-HK/Applying-DRL-to-HP-Model-for-Protein-Structure-Prediction

Source code and dataset for 2022 Publication "Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction"

Language: Python - Size: 30.6 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 2

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: 3 months ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 3

lightdock/lightdock-rust

A Rust implementation of the LightDock macromolecular docking software

Language: Rust - Size: 10.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 4

Bitbol-Lab/DiffPALM

Differentiable Pairing using Alignment-based Language Models

Language: Jupyter Notebook - Size: 2.82 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 2

Galaxies99/alpha-protein

Alpha-Protein: Protein Contact-map Prediction Boosted by Attention

Language: Python - Size: 4.76 MB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1

TommyGiak/HP_model

Implementation of the HP protein folding model with commands line interface

Language: Python - Size: 10.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

mircare/Porter5

Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes

Language: C++ - Size: 2.62 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 43 - Forks: 8

Bhattacharya-Lab/QDeep

Distance-based protein model quality estimation using deep ResNets

Language: Python - Size: 71.3 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 8 - Forks: 5

fpolticelli/tbblab_repository

List of useful resources for the Bioinformatics and Computational Biology field

Size: 133 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 5 - Forks: 2

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: almost 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 2

thuxugang/opus_rota5

OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer

Language: Python - Size: 25.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 2

Galaxies99/GANcon-pytorch 📦

personal RE-implementation of GANcon paper

Language: Python - Size: 78.1 KB - Last synced at: 7 months ago - Pushed at: about 2 years ago - Stars: 3 - 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: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

mufassirin/Multi-S3P

Multi-S3P: Protein Secondary Structure Prediction with Specialized Multi-Network and Self-Attention-based Deep Learning Model

Language: Python - Size: 89.8 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

libai1943/Protein-Structure-Optimization-via-Metaheuristics

A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model

Language: Matlab - Size: 5.78 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 5

msikorski93/Protein-Tertiary-Structure

Performing a regression task for estimating residue size based on given physicochemical properties of protein tertiary structures (CASP 5-9).

Language: Jupyter Notebook - Size: 1.27 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

elizaespinoza/modelsREV

Reticuloendotheliosis virus ENV, GAG and POL protein models.

Size: 2.82 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

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: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

ginevracoal/adversarial-protein-sequences

Code for paper "Adversarial Attacks on Protein Language Models", Ginevra Carbone, Francesca Cuturello, Luca Bortolussi, Alberto Cazzaniga (2022).

Language: Python - Size: 723 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

Bhattacharya-Lab/PolyFold

An interactive visual simulator for distance-based protein folding

Language: Java - Size: 646 MB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 24 - Forks: 6

Bhattacharya-Lab/SPECS

Superposition-based Protein Embedded CA SC score

Language: C++ - Size: 9.94 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 3

Bhattacharya-Lab/DisCovER

Distance- and orientation-based Covariational threadER

Language: C++ - Size: 17.7 MB - Last synced at: 9 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

Bhattacharya-Lab/rrQNet

Protein contact map quality estimation by evolutionary reconciliation

Language: Python - Size: 20.7 MB - Last synced at: 9 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

Bhattacharya-Lab/DConStruct

Hybridized distance- and contact-based hierarchical protein folding

Language: Python - Size: 371 KB - Last synced at: 9 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

YoannPa/Django_for_Prediction_of_Proteins_PPII

Language: C - Size: 21.3 MB - Last synced at: over 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

danielvarela/RosettaEvolution

Evolutionary Computation methods applied to protein structure prediction and protein folding modeling with the Rosetta Software Suite

Language: C++ - Size: 486 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 0

emanuele-progr/PSSP

Protein Secondary Structure Prediction project with RNNs and Transformers

Language: Python - Size: 626 KB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

psipred/fragfold

Fragment assembly ab initio protein folding

Language: C - Size: 11.9 MB - Last synced at: over 1 year ago - Pushed at: almost 9 years ago - Stars: 3 - Forks: 0

Dreycey/DebruijnExtend

This repository contains the source code for the DebruijnExtend tool. This tool uses known secondary structures for common protein kmers to predict the most likely secondary structure. This is done using a debruijn graph approach to incorporate local homology for predicting the most probable secondary structure along a protein. Tested on mac/linux

Language: Jupyter Notebook - Size: 66.6 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

amitkp57/deep-learning-protein-structure-prediction

Deep Learning for Protein Structure Prediction

Language: Jupyter Notebook - Size: 592 KB - Last synced at: 4 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

liponan/structure-generator

A machine learning model that builds amino acids into a protein model.

Language: Python - Size: 50.8 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 2

danielvarela/PSPHybridDE

Protein Structure prediction using Hybrid Differential Evolution (HybridDE)

Language: Python - Size: 7.81 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1

kleinhenz/psifold

Transformer model for protein structure prediction

Language: Python - Size: 174 KB - Last synced at: 5 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

poluyan/PEPSGO

Peptide structure prediction by global optimization of a potential energy function

Language: C++ - Size: 3.51 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

andreepdias/NelderMeadGPU

Implementação do algortimo Nelder-Mead em CUDA C++.

Language: Cuda - Size: 15.1 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

andreepdias/RMSDfrom3DAB

Algoritmo para o cálculo de RMSD para proteínas otimizadas com o modelo 3D AB Off-Lattice.

Language: Python - Size: 3.36 MB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

ShuklaGroup/FingerprintContacts

Source code for the manuscript: FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution

Language: Python - Size: 9.77 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

sailfish009/rgn Fork of aqlaboratory/rgn

Recurrent Geometric Networks for end-to-end differentiable learning of protein structure

Size: 34.7 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

chuankaizhao/SAXS-guidedAdaptiveSampling Fork of ShuklaGroup/SAXS-guidedAdaptiveSampling

Python implementation of Markov state model-based adaptive sampling guided by SAXS and hybrid information.

Language: Jupyter Notebook - Size: 1.16 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0