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.

Repository of 3D structural data of large biological molecules.

The collection of functional information on proteins.

Database of 3D protein structures.

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.

Drug Gene InteractionDGIdb - A database of drug-gene interactions and the druggable genome.Comparative Toxicogenomics Database - A database of Chemical-gene interactions, Chemical-disease associations, Gene-disease associations, and Chemical-phenotype associations.SNAP - A dataset which contains Drug-gene inter…

Knowledge GraphDrug 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.

A software of cheminformatics and Machine Learning.

High-performance spatial transcriptomics deconvolution. Processes 1M spots in ~3 minutes.

A software of cheminformatics and Machine Learning.

MCP server enabling spatial transcriptomics analysis via natural language.

scRNA analysis library in Python.

scRNA analysis library in R.

Spatial single cell analysis library in Python.

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

GCN + heterogeneous network

Autoencoder + Fully Connected NN

Multi-view embedding NN.

GNN Embedding + Attention

A DL Library for Drug Repurposing.

A library for Drug Target Interaction.

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

A library for Compound Protein Interaction prediction using Transformer.

a library for protein embeddings.

a library for chemical embeddingg and prediction.

LLM for chemical and molecule science

LLM for Biomedical text generation

LLM for biomedical information with several API.

foundation LLM for single cell data

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

A large-scale pretrained foundation model for single-cell gene expression data, enabling multiple downstream analysis tasks.

A transformer-based foundation model pretrained on millions of single-cell profiles to support various single-cell analysis tasks.

A foundation model pretrained on large-scale bulk RNA-seq data to learn general transcriptomic representations for downstream analysis tasks.