Dy1365/smiles2dta-demo

A Streamlit app for predicting drug-target binding affinity using a trained CNN model. Input SMILES strings and protein sequences for fast and accurate predictions.

Size: 1.95 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

hasanulmukit/smiles2dta-demo

A Streamlit app for predicting drug-target binding affinity using a trained CNN model. Input SMILES strings and protein sequences for fast and accurate predictions.

Language: Jupyter Notebook - Size: 18.1 MB - Last synced at: 4 days ago - Pushed at: 16 days ago - Stars: 3 - Forks: 0

instadeepai/protein-sequence-bfn

Supporting code for our paper "Protein Sequence Modelling with Bayesian Flow Networks"

Language: Python - Size: 1.02 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 32 - Forks: 2

chao1224/ProteinDT

A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)

Language: Python - Size: 19.4 MB - Last synced at: 19 days ago - Pushed at: 3 months ago - Stars: 66 - Forks: 6

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

tbepler/protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

Language: Python - Size: 50.8 KB - Last synced at: 11 days ago - Pushed at: almost 4 years ago - Stars: 260 - Forks: 75

VarunUllanat/mint

Learning the language of protein-protein interactions

Language: Python - Size: 3.59 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 56 - Forks: 4

ostrokach/proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Language: Jupyter Notebook - Size: 271 MB - Last synced at: 14 days ago - Pushed at: about 4 years ago - Stars: 59 - Forks: 8

aqlaboratory/proteinnet

Standardized data set for machine learning of protein structure

Language: Python - Size: 223 KB - Last synced at: 16 days ago - Pushed at: over 4 years ago - Stars: 886 - Forks: 130

ISDementyev/pmUE

pmUE (Protein Modelling Unreal Engine) - a repo for constructing a molecule visualizer plugin in Unreal

Language: C++ - Size: 37.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 3

aziele/pairwise-sequence-alignment

A Python module to calculate alignment between two sequences using EMBOSS' needle, stretcher, and water

Language: Python - Size: 44.9 KB - Last synced at: 25 days ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 3

MartinThoma/propy3

A Python 3 version of the protein descriptor package propy

Language: Python - Size: 960 KB - Last synced at: 6 days ago - Pushed at: about 2 years ago - Stars: 41 - Forks: 13

aziele/fastapy

A lightweight Python module to read and write FASTA sequence records

Language: Python - Size: 58.6 KB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 6 - Forks: 2

ISYSLAB-HUST/ProtFlash

ProtFlash: A lightweight protein language model

Language: Python - Size: 21.5 KB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 104 - Forks: 3

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

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Size: 51.8 KB - Last synced at: 5 days ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 0

dohlee/pifold-pytorch

An unofficial re-implementation of PiFold, a fast inverse-folding algorithm for protein sequence design, in PyTorch.

Language: Jupyter Notebook - Size: 152 KB - Last synced at: 15 days ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

cusbg/MolArt

MOLeculAR structure annoTator

Language: JavaScript - Size: 58.5 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 34 - Forks: 8

westlake-repl/SaProt

[ICLR'24 spotlight] Saprot: Protein Language Model with Structural Alphabet

Language: Python - Size: 2.45 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 332 - Forks: 32

PeptoneLtd/pepkalc

Robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded state.

Language: Python - Size: 24.4 KB - Last synced at: about 5 hours ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 1

michalbukowski/pfam-genomes

Snakemake pipeline for searching genomic sequences for those that encode proteins containing domains of choice

Language: Python - Size: 216 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

codecreatede/panache-extract

maf to panache and extracting all snps and pangenome specific information.

Language: Ruby - Size: 8.79 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

PNNL-Comp-Mass-Spec/protein-coverage-summarizer

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

Language: C# - Size: 35.1 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 6 - Forks: 3

RG-10/RG-10.github.io

🌱🌟 My Personal Portfolio 🌟🌱

Language: JavaScript - Size: 8.54 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

jaumebonet/RosettaSilentToolbox

Python Toolbox For Rosetta Silent Files Processing

Language: Python - Size: 389 MB - Last synced at: 14 days ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 9

psipred/DMPfold

De novo protein structure prediction using iteratively predicted structural constraints

Language: C - Size: 195 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 55 - Forks: 16

Shen-Lab/Fold2Seq-icml2021 Fork of IBM/fold2seq

[ICML 2021] "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design" by Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen

Language: Python - Size: 4.85 MB - Last synced at: 12 months ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 1

IbrahimTanyalcin/I-PV

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

Language: HTML - Size: 66.6 MB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 10 - Forks: 1

kris96tian/translate_dna_app

Code for DNA translation to proteins through a web interface. It uses Flask for the web aspects and defines the logic to translate codons based on genetic code rules. Users can interactively enter DNA-seq on a web form and see the protein output.

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

sinc-lab/Comparison-of-Protein-learning

Comparison of protein learning

Language: Jupyter Notebook - Size: 17.7 MB - Last synced at: 9 months ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 1

jendelel/PrankWebApp

Web application for protein-ligand binding sites analysis and visualization

Language: JavaScript - Size: 13.8 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 6

LPDI-EPFL/rstoolbox Fork of jaumebonet/RosettaSilentToolbox

Python Toolbox For Rosetta Silent Files Processing

Language: Python - Size: 389 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 14 - Forks: 4

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

haichengyi/bioseq2vec

BioSeq2vec: learning deep representation of biological sequences using LSTM Encoder-Decoder

Language: Python - Size: 80.3 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 4

bhi-kimlab/DeepFam

Deep learning based alignment-free method for protein family modeling and prediction

Language: Python - Size: 3.04 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 16 - Forks: 8

kalarimonk/Probhujina

Visualizing protein structures with their sequences!!!

Language: C++ - Size: 48.8 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

dissipative/ribosome

The Ribosome package is a Go library designed for efficient transcription and translation of DNA and RNA sequences, inspired by the real processes in living cells.

Language: Go - Size: 71.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Shen-Lab/gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

Language: Roff - Size: 334 MB - Last synced at: 12 months ago - Pushed at: about 4 years ago - Stars: 36 - Forks: 7

kn-bibs/dotplot

Simple visualisation tool for sequences' similarity in bioinformatics

Language: Python - Size: 210 KB - Last synced at: 10 days ago - Pushed at: about 7 years ago - Stars: 13 - Forks: 2

lukaszsobala/spike-annotation 📦

Annotation of SARS-CoV-2 Spike glycoprotein

Size: 88.9 KB - Last synced at: 2 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

0xpranjal/COVID-Genome-Computational-Analysis

Computational predictions of protein attributes associated with COVID-19 using Data Science techniques

Language: Jupyter Notebook - Size: 1.96 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 5

kaledhoshme123/Using-Deep-Learning-to-Annotate-the-Protein-Universe

Understanding the relationship between amino acid sequence and protein function is a long-standing problem in molecular biology with far-reaching scientific implications.

Language: Jupyter Notebook - Size: 595 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

zmmason/BINF

Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

Language: Python - Size: 86.9 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 1

DSIMB/MEDUSA

A Deep Learning based protein flexibility prediction tool.

Language: Perl - Size: 121 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2

johnnytam100/FPredX

FPredX

Language: Python - Size: 36.1 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

changlabtw/MS2CNN

Language: Python - Size: 96.2 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 3

mtp-usz/IsoAligner Fork of JacobHanimann/IsoAligner

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

Language: Python - Size: 215 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - 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: about 2 years ago - Pushed at: about 4 years ago - Stars: 4 - Forks: 2

neelotpal-d/DNA_Protein_Translation

Program for Translation from DNA sequence to protein sequence

Language: C - Size: 752 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

YoannPa/Threading-PU

Alignement structurale d'une séquence protéique sur une structure protéique 3D.

Language: Python - Size: 1.36 MB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

ratvec/results

Results from application of RatVec to protein sequences

Language: Jupyter Notebook - Size: 161 KB - Last synced at: 12 months ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0

acgtun/hsearch

HSEARCH: fast and accurate protein sequence motif search and clustering

Language: C++ - Size: 3.66 MB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

acgtun/s3

S3: Sequence Similarity Search (Protein Sequence)

Language: C++ - Size: 120 KB - Last synced at: about 2 years ago - Pushed at: almost 9 years ago - Stars: 0 - Forks: 0