awesome-computational-biology

Public functional genemics database

Public database for single cell RNA

Public database for single cell RNA

One of the biggest chemical database such as compounds, genes and proteins

Chemical database focused on small chemical compounds

Database of bioactive molecules with drug-like properties

Chemical structure database

Collection of small molecules and biopolymers

Database of lipids

Database of chemical reactions

Collections of drug repurposing data containing drug, moa, target etc

collections of drug-target, target-disease, and drug-disease dataset

Free database of commercially-available compounds for virtual screening

Benchmark for molecular machine learning

Dataset for predicting mutagenicity

Database for antibody-drug conjugates

Database of Pathways and Interactions

Collection fo drawn pathway maps

Database of biological pathways

Open souce databases and tools for mass spectrometry reference spectra

Meta database of metabolite mass spectra, metadata and associated compounds

One of the biggest human protein database contained cells, tissues, and organs

Database of the 3D shapes of proteins, nucleic acids, and complex assemblies

The collection of functional information on proteins

Database of 3D protein structures

Repository of 3D structural data of large biological molecules

Experiment for advancing the methods of predicting protein structure from sequence

Collection of clustered protein sequence databases

Hierarchical classification of protein domain structures

Database of image, proteomics, transcriptomics and systems biology

Database of genetic sequence offered by NCBI

Genome blowser offered by UCSC

Database of Cancer Genomics. This has overall metaview for a lot of patients

Collection of single-cell datasets

Resource for studying human gene expression and regulation

Genome-wide CRISPR-Cas9 screens in cancer cell lines

Comprehensive resource for exploring somatic mutations in human cancers

Free resource for archiving, analysis, and browsing of metagenomic and metatranscriptomic data

Open-access database of curated, non-redundant transcription factor binding profiles

Comprehensive drug information resource for approved drugs

A database of drug and target maintained by the University of Alberta

A database of drug-gene interactions and the druggable genome

A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations

A dataset which contains Drug-gene interactions

A database for a lot of tasks such as drug-target, drug-response, drug-drug interaction

A database which focus on 60 cancer cell lines with many drugs

A database of drug sensitibity which has 1000 human cancer cell lines and 100s compounds

A database of cancer cell lines. This has 1000 cell lines

Integration of multiple cancer cell line databases

A database of Chemical Protein Interaction

A database of compounds and targes

Database of experimentally measured binding affinity data for biomolecular complexes

Large-scale dataset for machine learning in structure-based virtual screening

Protein-Protein Interaction Networks for several organisms

Database of Protein, Genetic and Chemical Interactions

Human Protein-Protein Interaction database

Drug Mechanism Database (DrugMechDB)

: database of the mechanism of action from a drug to a disease

DRKG

A library for biological knowledge graph

Database of privately and publicly funded clinical studies

International Classification of Diseases, 10th revision

European database of clinical trials

Freely accessible critical care database

: API for searching articles in PubMed

Chemistry Development Kit

A software of cheminformatics and Machine Learning

RDKit

A software of cheminformatics and Machine Learning

scRNA analysis library in Python

scRNA analysis library in R

drGAT

: A model for drug response prediction with gene explainability with attention mechanism

MOFGCN

: GCN + heterogeneous network

: Autoencoder + Fully Connected NN

DGDRP

: Multi-view embedding NN

DeepAEG

: GNN Embedding + Attention

DeepPurpose

A DL Library for Drug Repurposing

NeoDTI

A library for Drug Target Interaction

MCPINN

A library for drug discovery using Compound Protein Interaction and Machine Learning

TransformerCPI

A library for Compound Protein Interaction prediction using Transformer

Evolutionary Scale Modeling

a library for protein embeddings

ChemBERTa-2

a library for chemical embeddingg and prediction

LLM for chemical and molecule science

BioGPT

LLM for Biomedical text generation

GeneGPT

LLM for biomedical information with several API

GenePT

foundation LLM for single cell data

scPRINT

scPRINT is pretrained on 50M cells to denoise and perform zero imputation of any single cell RNAseq profile