Hacettepe University Biological Data Science Laboratory

Public

26 repositories

DrugGEN
Public
Official implementation of DrugGEN: Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
machine-learning deep-learning pytorch transformer generative-adversarial-network drug-discovery generative-models graph-neural-networks drug-target-interactions denovo-design
Python
•
GNU General Public License v3.0
•17•56•4•0•Updated Mar 12, 2025Mar 12, 2025
CROssBAR_LLM
Public
JavaScript
•0•3•0•0•Updated Mar 11, 2025Mar 11, 2025
ProtMamba
Public
Python
•0•1•0•0•Updated Mar 10, 2025Mar 10, 2025
CROssBARv2
Public
This is a repo for migration of CROssBAR data to the Neo4j database via BioCypher
bioinformatics knowledge-graph
Python
•7•8•1•0•Updated Mar 7, 2025Mar 7, 2025
DEEPScreen2
Public
Automated Tool for Drug-Target Interaction Prediction Using Deep Convolutional Neural Networks
Python
•
GNU General Public License v3.0
•3•1•0•4•Updated Mar 6, 2025Mar 6, 2025
Prot2Mol
Public
Target based molecule generation using protein embeddings and SELFIES molecule representation
Python
•
GNU General Public License v3.0
•2•0•0•0•Updated Feb 25, 2025Feb 25, 2025
ProtHGT
Public
A Heterogeneous Graph Transformer (HGT)-based model for protein function prediction using biological knowledge graphs and protein language models
knowledge-graph gene-ontology hgt protein-function-prediction gene-ontology-terms heterogeneous-graph-learning protein-language-model heterogeneous-graph-transformer biological-knowledge-graph
Python
•
GNU General Public License v3.0
•0•2•0•0•Updated Feb 6, 2025Feb 6, 2025
HoliLoc
Public
HoliLoc: Image, Sequence, and Interactome Based Prediction of Protein Subcellular Localization
Python
•
GNU General Public License v3.0
•1•0•0•0•Updated Jan 8, 2025Jan 8, 2025
CROssBAR-pypath
Public
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
Python
•
GNU General Public License v3.0
•48•0•0•0•Updated Jan 7, 2025Jan 7, 2025
crossbar-graphql
Public
JavaScript
•
GNU General Public License v3.0
•0•0•0•0•Updated Dec 12, 2024Dec 12, 2024
SELFormer
Public
SELFormer: Molecular Representation Learning via SELFIES Language Models
machine-learning deep-learning cheminformatics transformers drug-discovery representation-learning language-model
Python
•17•88•1•0•Updated Dec 1, 2024Dec 1, 2024
DeepResponse
Public
DeepResponse: Large Scale Prediction of Cancer Cell Line Drug Response with Deep Learning Based Pharmacogenomic Modelling
machine-learning deep-learning convolutional-neural-networks cancer-research multi-omics graph-neural-networks drug-response-prediction graph-transformer
Python
•3•1•0•0•Updated Oct 28, 2024Oct 28, 2024
crossbar-website
Public
JavaScript
•0•0•0•0•Updated Oct 18, 2024Oct 18, 2024
Domain2GO
Public
A Python tool for predicting protein functions by associating domains with Gene Ontology terms using existing domain and GO annotation data
protein-function-prediction
Python
•1•1•0•0•Updated Aug 12, 2024Aug 12, 2024
ASCARIS
Public
ASCARIS: Annotation & Structure-Based Representation of SAVs
Python
•3•2•0•0•Updated Jul 22, 2024Jul 22, 2024
SELFormer_back
Public
SELFormer: Molecular Representation Learning via SELFIES Language Models
Python
•3•4•0•0•Updated Jun 29, 2024Jun 29, 2024
SELFormerv2
Public
Python
•1•0•0•0•Updated Jun 4, 2024Jun 4, 2024
ProtBENCH
Public
Python
•
GNU General Public License v3.0
•3•11•0•0•Updated May 21, 2024May 21, 2024
CROssBAR-Data-Process
Public
CROssBAR v2 GraphDB Data Process
Python
•2•0•0•1•Updated Jan 25, 2024Jan 25, 2024
TransPRSFP
Public
Python
•
GNU General Public License v3.0
•2•0•0•0•Updated Oct 5, 2023Oct 5, 2023
CROssBARv1
Public
Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations
PHP
•
Other
•11•0•0•0•Updated Jun 22, 2023Jun 22, 2023
website
Public
Website for HU Biological Data Science Laboratory
Astro
•
MIT License
•0•2•0•0•Updated May 23, 2023May 23, 2023
DrugApp
Public
Python
•
GNU General Public License v3.0
•1•8•0•0•Updated Dec 14, 2022Dec 14, 2022
awesome-denovo-papers
Public
Awesome De novo drugs design papers
12•4•0•0•Updated Sep 6, 2022Sep 6, 2022
DRUIDom
Public
DRUIDom (DRUg Interacting Domains): a computational method for predicting new drug/compound - target protein interactions for drug discovery and repurposing, via mapping ligands to structural domains
MATLAB
•
GNU General Public License v3.0
•3•0•0•0•Updated Dec 6, 2021Dec 6, 2021
HPO2GO
Public
Mapping between HPO and GO terms
MATLAB
•
GNU General Public License v3.0
•3•0•0•0•Updated Mar 26, 2020Mar 26, 2020