BIOINFORMATICS / AI / DISCOVERY
Explore the frontier.Find your next step.
Discover data, tools, and methods across bioinformatics and AI. Follow a research question to a reliable starting point.
THE TOOLKIT
Good research starts with good tools.
UniProt
Find protein sequences, functional annotations and identifier mappings, with links to related biological data.
RCSB PDB
Search, view and download macromolecular structures alongside their experimental context.
AlphaFold DB
Explore predicted protein structures and confidence information, with downloadable models for further study.
ColabFold
Run protein structure prediction through notebooks or local batch tools, connecting sequence search with modeling.
Scanpy
Analyze single-cell data in Python, from preprocessing and visualization to clustering and differential expression.
Bioconductor
An R-centered ecosystem of analysis packages, annotations and reproducible workflows for biological data.
Ensembl
Explore genomes, gene annotations, variation and comparative genomics in a shared browsing environment.
CZ CELLxGENE Census
A public single-cell RNA data resource. Query cells and genes, then bring selected data into Python or R.
Virtual Cells Platform
Explore biological datasets, AI models and task benchmarks through a shared platform for model use and evaluation.
scGPT
Use pretrained models for single-cell analysis, including cell representations, annotation and perturbation prediction.
Pertpy
Analyze single-cell perturbation experiments, organize data and metadata, and compare cellular responses to perturbations.
nf-core
Community-maintained Nextflow pipelines and components for portable, reproducible bioinformatics analysis.
Galaxy
Build analyses in a web interface, keep a record of each step and share data, results and workflows.
READ & UNDERSTAND
Behind the methods
Reading and practical notes connecting tools, context, and methodological choices.
AI virtual cells: How close are we to growing a cell in a computer?
A review of virtual-cell research, from cell foundation models and mechanistic whole-cell simulations to morphology, metabolism, spatial interactions, tissues and embryos. It surveys public data, code and benchmarks, distinguishing validated capabilities from research goals, with references and practical starting points.
AlphaFold 3 v3.0.4: running on CPUs and Apple Silicon
A version-pinned guide to AlphaFold 3 on Linux GPUs, CPUs, and Apple Silicon, including installation, storage requirements, experimental backends, and limitations.
BindCraft2 v1.0.4: antibody interfaces, conformation filters, and rerun guidance
A guide to BindCraft2 v1.0.4 changes in antibody interfaces, induced-fit and fold-switching filters, and large-system execution, with the limits of the reported computational examples.
OPEN TO DISCOVERY
Help the next useful resource get found.
Recommend a tool, suggest a correction, or discuss editorial collaboration.