OPIG
IPD
Meta AI 
Biohub
Arc Institute
Google DeepMind
Arc Institute
RosettaCommons
RCSB
USC
Genomic Intelligence
ByteDance
EMBL-EBI
Biohub
NCBI
UW
Google DeepMind
Rutgers University 
Columbia University
RIMD
libnano
UNR UW 
UQ 
UCSD
Proto
Dunbrack Lab
Broad Institute 
The Jackson Laboratory 
Yale University
Calico
UCSF 
Autosome.org
NCBI
Google DeepMind
NVIDIA Arc Institute UCSF
Boltz 
MIT Jameel Clinic 
Recursion
Profluent
SIB EMBL-EBI 
PIR
MSKCC
PDBe EMBL-EBI 
wwPDB
UT Southwestern 
St. Jude
Steinegger Lab
Arc Institute
Chai Discovery
NCBI
NCBI
Biohub
Proto
IPD
Microsoft Research
Google DeepMind
Steinegger Lab
Meta AI
IPD
Aureka AI Research
IPD
Meta AI Biohub
Steinegger Lab 
Söding Lab
EMBL-EBI
Biohub
TBI Vienna
Scripps Research 
Forli Lab
Salesforce Research
Google DeepMind
Google DeepMind EMBL-EBI OPIG IPD Meta AI Biohub Arc Institute Google DeepMind Arc Institute RosettaCommons RCSB USCGenomic Intelligence
ByteDance EMBL-EBI Biohub NCBI UW Google DeepMind Rutgers University Columbia University RIMD libnano UNR UW UQ UCSD Proto Dunbrack Lab Broad Institute The Jackson Laboratory Yale University Calico UCSF Autosome.org NCBI Google DeepMind NVIDIA Arc Institute UCSF Boltz MIT Jameel Clinic Recursion Profluent SIB EMBL-EBI PIR MSKCC PDBe EMBL-EBI wwPDB UT Southwestern St. Jude Steinegger Lab Arc Institute Chai Discovery NCBI NCBI Biohub Proto IPD Microsoft Research Google DeepMind Steinegger Lab Meta AI IPD Aureka AI Research IPD Meta AI Biohub Steinegger Lab Söding Lab EMBL-EBI Biohub TBI Vienna Scripps Research Forli Lab Salesforce Research Google DeepMind Google DeepMind EMBL-EBIThe Open-Source Infrastructure Layer for Biology
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Proto Tools
A lot of computational biology looks like this: find a tool that does what you need, spend half a day getting it to install, spend another day figuring out how to call it, then reformat the output so the next tool can use it. Every tool has its own opinions about Python versions, CUDA, weight paths, and input formats.Proto Tools implements these tools so they all behave the same way. Each one is a Python function with a Pydantic input and output. Fold a protein with AlphaFold3, sample sequences with ProteinMPNN, search with BLAST; the shape of the call is the same, and the first invocation quietly sets up the environment and weights in isolation.Use it on its own, or as the tools layer of the broader Proto framework.Key Features
A quick tour of what proto-tools handles for you. Each card opens a deeper guide.Unified Interface
Consistent Python APIs with standardized Pydantic Input/Config/Output models across all tools
Isolated Environments
Each tool gets its own virtual environment; weights and dependencies are fetched and cached on first use
Device Management
Automatic GPU allocation, LRU eviction, and multi-GPU routing
Parallel Execution
Fan a single tool call out across every visible GPU with ToolPool
Tool Catalog
Every tool we implement, at a glance. Select any to open its page.Get Started
Installation
Set up the package and optional dependencies
Quickstart
Run your first tool in 5 minutes
Concepts
Understand the tool pattern and execution model