Steinegger Lab 
Söding Lab
Proto
Steinegger Lab
Institute for Protein Design
Oxford Protein Informatics Group (OPIG)
Proto
EMBL-EBI
Microsoft Research
Meta AI 
Biohub
Steinegger Lab
Google DeepMind
RosettaCommons
Calico
Broad Institute 
The Jackson Laboratory 
Yale University
Biohub
Salesforce Research
Memorial Sloan Kettering Cancer Center
Biohub
Arc Institute
Arc Institute
Google DeepMind EMBL-EBI
Institute for Protein Design
NCBI
Chai Discovery
Google DeepMind
SIB EMBL-EBI 
PIR
University of Nevada, Reno University of Washington University of Queensland University of California, San Diego
Google DeepMind
PDBe EMBL-EBI 
wwPDB
Meta AI
Profluent
NCBI
Boltz 
MIT Jameel Clinic 
Recursion
Google DeepMind
NCBI
Institute for Protein Design
ByteDance
Meta AI Biohub
UT Southwestern Medical Center 
St. Jude Children’s Research Hospital
EMBL-EBI
RIMD
Google DeepMind
Biohub
NCBI
TBI Vienna
RCSB
Institute for Protein Design
Dunbrack Lab
Arc Institute Steinegger Lab Söding Lab Proto Steinegger Lab Institute for Protein Design Oxford Protein Informatics Group (OPIG) Proto EMBL-EBI Microsoft Research Meta AI Biohub Steinegger Lab Google DeepMind RosettaCommons Calico Broad Institute The Jackson Laboratory Yale University Biohub Salesforce Research Memorial Sloan Kettering Cancer Center Biohub Arc Institute Arc Institute Google DeepMind EMBL-EBI Institute for Protein Design NCBI Chai Discovery Google DeepMind SIB EMBL-EBI PIRUniversity of Nevada, Reno University of Washington University of Queensland University of California, San Diego
Google DeepMind PDBe EMBL-EBI wwPDB Meta AI Profluent NCBI Boltz MIT Jameel Clinic Recursion Google DeepMind NCBI Institute for Protein Design ByteDance Meta AI Biohub UT Southwestern Medical Center St. Jude Children’s Research Hospital EMBL-EBI RIMD Google DeepMind Biohub NCBI TBI ViennaRCSB
Institute for Protein DesignDunbrack Lab
Arc InstituteThe Open-Source Infrastructure Layer for Biology
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