PHENIX

Info

PHENIX is a comprehensive software package for macromolecular structure determination using X-ray crystallography (including neutron and electron diffraction) and cryo-EM data. Development began ~1999 at Lawrence Berkeley National Laboratory (LBNL). ~35,000 users; 70+ commercial licensees including major pharma/biotech. Highest grossing software product ever developed at Berkeley Lab ($7.7M in royalties).

Development Team (multi-institutional)

• LBNL (Paul Adams’s group)
• New Mexico Consortium / Los Alamos National Laboratory (Tom Terwilliger’s group)
• University of Cambridge (Randy Read’s group)
• Duke University (David and Jane Richardson’s group)
• UTHealth (Matt Baker’s group)

People

Name	Role	Affiliation
Paul Adams	PI / Lead; Assoc. Lab Director for Biosciences	LBNL
Tom Terwilliger	Co-PI	Los Alamos National Laboratory / New Mexico Consortium
Randy Read	Co-PI	University of Cambridge
Jane Richardson	Co-PI	Duke University
David Richardson	Co-PI	Duke University
Matt Baker	Co-PI	UTHealth
Pavel Afonine	Key developer	LBNL
Nigel Moriarty	Key developer	LBNL

Funding

• NIH (primary, long-standing support)
• Initial development funded by Berkeley Lab LDRD
• Commercial license revenue via Phenix Consortium (industrial partners)

Note on Paul Adams

Paul Adams is also on the wwPDB Advisory Committee representing RCSB PDB. He is a major node connecting crystallography software development to PDB governance. His dual role as LBNL Assoc. Lab Director and PHENIX lead makes him a key power broker in the landscape.

Key Relationships

• Paul Adams also sits on RCSB PDB advisory committee
• Software interoperates with Coot, PyMOL, and planned integration with ChimeraX
• Contributed to COVID vaccine development (cryo-EM analysis of spike protein for BioNTech/Pfizer)
• Collaboration with Nobel laureate David Baker on Rosetta integration
• Overlaps with CCP4 in refinement and model building functionality

Key Reference

Liebschner et al., Acta Cryst D75 (2019), 861-877. doi:10.1107/S2059798319011471