Landscape Directory

Data Archives and Governance

The wwPDB is the central governing body for structural biology data. Its member archives are the definitive repositories for the field:

• RCSB PDB — US data center (Rutgers/UCSD/UCSF), led by Stephen K. Burley
• PDBe (UK, EMBL-EBI) — European data center, led by Sameer Velankar; also leads AlphaFold DB and 3D-Beacons
• PDBj (Japan, Osaka University) — Asia-Pacific data center, led by Genji Kurisu
• PDBc (China, ShanghaiTech) — Newest wwPDB associate member, represented by Wenqing Xu
• BMRB — NMR spectroscopy data archive (UConn Health), led by Jeffrey Hoch
• EMDB — Electron microscopy map archive (EMBL-EBI), led by Kyle Morris
• EMPIAR — Raw cryo-EM image archive
• OneDep — wwPDB unified deposition, validation, and biocuration system

The PDB-IHM extension handles integrative and hybrid models (Dr. Andrej Sali, Helen M. Berman).

Software Consortia

Two major multi-institutional consortia develop the dominant MX software stacks:

PHENIX Consortium (US-led)

Led by Paul Adams at LBNL. Partners: University of Cambridge (Randy Read, Airlie McCoy — Phaser), Duke University (Jane S. Richardson, Vincent Chen, Christopher Williams — MolProbity), Los Alamos National Laboratory (Thomas Terwilliger), UTHealth (Matt Baker — cryo-EM). Built on the cctbx open-source foundation.

CCP4 Consortium (UK-led)

Led by Eugene B. Krissinel and Charles Ballard at STFC Rutherford Appleton Laboratory. Key developers: Martyn Winn, Ronan Keegan (MrBUMP), Andrey Lebedev, Stuart McNicholas (Moorhen), Adam Simpkin (SIMBAD). Executive Committee chaired by Ivo Tews. Refinement via Garib Murshudov’s REFMAC5 at MRC-LMB, with current-gen work by Rob Nicholls.

US Institutional Power Centers

• LBNL / ALS — PHENIX (Paul Adams), DIALS US side (Aaron Brewster, Nicholas Sauter), ALS beamlines (James Holton). Adams is Associate Lab Director for Biosciences.
• UCSF — DiffUSE PI Jaime Fraser, cryo-EM pioneer Yifan Cheng (HHMI), integrative modeling Dr. Andrej Sali (IMP, PDB-IHM), deep mutational scanning Willow Coyote-Maestas.
• Rutgers — RCSB PDB (Stephen K. Burley), Helen M. Berman (Emerita), David Case (AMBER), John Westbrook.
• Duke University — Richardson Lab: Jane S. Richardson, Vincent Chen, Christopher Williams, W. Bryan Arendall, III (MolProbity, validation).
• University of Washington — Institute for Protein Design: David Baker (Nobel 2024), Rohith Krishna (RFdiffusion), William H. Sheffler (RosettaHoles). Rosetta lineage.
• Cornell / CHESS — Nozomi Ando (diffuse scattering, DiffUSE team), Steve Meisburger, Richard Gillilan.
• Los Alamos National Laboratory — Thomas Terwilliger (PHENIX / SOLVE/RESOLVE), Li-Wei Hung, Michael Wall (DiffUSE team, diffuse scattering MD simulations).
• APS / Argonne — Andrzej Joachimiak (Structural Biology Center), Janet L. Smith (LS-CAT at APS), Raymond Osborn.
• Stanford / SLAC — Axel T. Brunger (XPLOR/CNS lineage, HHMI), Polly Fordyce (high-throughput biophysics), TJ Lane (MD + X-ray scattering), Ariana Peck (diffuse scattering models).
• UConn Health — Jeffrey Hoch (BMRB, NMRbox, NAN).
• St. Jude — Marcus Fischer (room-temp multi-conformer crystallography, FLEXR), Madan Babu (SVP/Chief Data Scientist, IDPs, formerly MRC-LMB).
• CUNY — Daniel Keedy (qFit, multi-conformer modeling).
• Flatiron Institute — Pilar Cossio (Bayesian cryo-EM, conformational heterogeneity).
• NIH — Charles Schwieters (XPLOR-NIH), Marius Clore.

International nodes (concise)

• MRC-LMB (Cambridge, UK) — Sjors Scheres (RELION), Garib Murshudov (REFMAC5), Paul Emsley (Coot), Rob Nicholls, John Briggs, Venki Ramakrishnan (Nobel 2009).
• Diamond Light Source / Harwell (UK) — CCP4 core team, DIALS UK, XChem (Frank von Delft), Martin Walsh, Gwyndaf Evans.
• EMBL-EBI (Hinxton, UK) — PDBe, EMDB, EMPIAR, AlphaFold DB, ELIXIR hub.
• Cambridge CIMR (UK) — Randy Read, Airlie McCoy (Phaser).
• York YSBL (UK) — Jon Agirre (Privateer), Stuart McNicholas (Moorhen), Kevin Cowtan, Eleanor Dodson.
• Hamburg (Germany) — Andrea Thorn (AUSPEX/HARUSPEX), Helen Ginn (DESY), Kartik Ayyer (MPSD).
• Osaka University (Japan) — Genji Kurisu (PDBj).

DiffUSE and Protein Dynamics

The DiffUSE project ($5M, Astera Institute) aims to make diffuse X-ray scattering accessible as a probe of protein dynamics:

DiffUSE team (per diffuse.science/members)

• Jaime Fraser (PI, UCSF), Nozomi Ando (Cornell/CHESS), James Holton (ALS), Steve Meisburger (CHESS), Michael Wall (LANL), Stephanie Wankowicz (Scientific Program Director, Vanderbilt)

Multi-conformer modeling community

• Daniel Keedy — qFit (CUNY)
• Marcus Fischer — FLEXR (St. Jude)
• Stephanie Wankowicz — qFit contributor (Vanderbilt / DiffUSE)

Dynamics methods (potential collaborators)

• Hannah Wayment-Steele — AF2 multi-state dynamics (UW-Madison)
• TJ Lane — MD + X-ray scattering (SLAC)
• Pilar Cossio — Bayesian cryo-EM heterogeneity (Flatiron)
• Polly Fordyce — high-throughput microfluidic biophysics (Stanford)
• Colin Jackson — enzyme evolution crystallography (ANU)
• Rohith Krishna — protein design / RFdiffusion (Baker Lab / UW)
• Willow Coyote-Maestas — deep mutational scanning (UCSF)
• Pedro Beltrao — structural proteomics / PTMs (ETH Zurich)
• Doeke Hekstra — time-resolved crystallography (Harvard)

Facilities and Light Sources

US synchrotrons and XFELs

• APS — Advanced Photon Source (Argonne); completed APS-U upgrade 2024
• CHESS — Cornell High Energy Synchrotron Source; $20M NSF precision X-ray beamline
• SSRL — Stanford Synchrotron Radiation Lightsource (+ LCLS/LCLS-II XFEL at SLAC)
• ALS — Advanced Light Source (Berkeley); ALS-U upgrade underway
• NSLS — National Synchrotron Light Source (Brookhaven)

International facilities

• Diamond Light Source — UK national synchrotron (Harwell)
• ESRF — European Synchrotron Radiation Facility (Grenoble)
• KEK / Photon Factory — Japan
• Paul Scherrer Institute / SLS — Switzerland

Software Ecosystem

Crystallography

• PHENIX — dominant US refinement suite (NIH funded)
• CCP4 — UK collaborative computational project (BBSRC)
• DIALS — modern open-source data processing (Diamond + LBNL + CCP4)
• Coot — model building (Paul Emsley, MRC-LMB)
• Phaser — molecular replacement (Randy Read, Airlie McCoy)
• HKL-2000 — data processing (Zbyszek Otwinowski, Wladek Minor)
• XDS — data processing (Wolfgang Kabsch)
• BUSTER-TNT — refinement (Gerard Bricogne, Global Phasing Ltd)

Validation

• MolProbity — all-atom structure validation (Jane S. Richardson, Duke)
• PDB-REDO — automated re-refinement (Robbie P. Joosten, Anastassis Perrakis)
• WHAT_CHECK — protein validation (Gert Vriend)
• OneDep — wwPDB deposition validation
• Privateer — glycan validation (Jon Agirre)

NMR

• XPLOR-NIH — NMR structure calculation (Charles Schwieters, Marius Clore)
• CCPN — collaborative computing project for NMR
• NMRbox — virtualised NMR software platform (Jeffrey Hoch)
• NMRPipe — processing pipeline (NIST)

Cryo-EM

• RELION — open-source (Sjors Scheres, MRC-LMB)
• cryoSPARC — commercial (Structura Biotechnology)
• cryoDRGN — ML conformational heterogeneity (Ellen Zhong, Princeton)

Protein design

• Rosetta / RFdiffusion — David Baker / Rohith Krishna (UW IPD)
• MODELLER / IMP — Dr. Andrej Sali (UCSF)

Visualization

• ChimeraX — UCSF
• PyMOL — Schrodinger (commercial)
• Mol* — web-based (EMBL-EBI + RCSB)

Conferences and Schools

• Erice International School of Crystallography — Ettore Majorana Foundation, Sicily. 2022: first diffuse scattering school (directed by Nozomi Ando + Andrew Goodwin). 2026: structural cell biology + ML.
• Gordon Research Conference on Diffraction Methods in Structural Biology — biennial
• CCP4 Study Weekend — annual UK MX workshop

Standards and Governance Bodies

• IUCr — International Union of Crystallography
• NIAC — NeXus data format governance (Aaron Brewster, Chair)
• ELIXIR — European life science data coordination
• Instruct-ERIC — Pan-European structural biology infrastructure
• CCDC — Cambridge Crystallographic Data Centre (small-molecule restraint libraries)
• HHMI — Howard Hughes Medical Institute (US research funding)

wwPDB Task Forces and Working Groups

• wwPDB task force-X-Ray Validation — Read et al. 2011
• wwPDB task force-EM Validation
• wwPDB task force-NMR Validation
• wwPDB task force-Small Angle Scattering (SAS)
• wwPDB task force-ModelCIF Working Group
• wwPDB task force-PDBx mmCIF Working Group
• wwPDB task force-Ligand Validation Workshop — Adams et al. 2016
• wwPDB task force-Hybrid Integrative Methods
• wwPDB task force-Validation Task Forces

Key People (bridging multiple institutions)

• Stephen K. Burley — RCSB PDB Director, wwPDB PI
• Paul Adams — PHENIX PI, LBNL Associate Lab Director, wwPDB AC
• Sameer Velankar — PDBe lead, AlphaFold DB, wwPDB PI
• Helen M. Berman — RCSB PDB Director Emerita, PDB co-founder
• Jeffrey Hoch — BMRB PI, NMRbox, NAN
• Jaime Fraser — DiffUSE PI, UCSF
• Nozomi Ando — DiffUSE team, Cornell/CHESS, 2022 Erice co-director
• John Rubinstein — wwPDB AC Chair, Hospital for Sick Children / University of Toronto
• Randy Read — Phaser, IUCr President, University of Cambridge
• Dr. Andrej Sali — IMP, PDB-IHM, UCSF
• David Baker — Rosetta, Nobel 2024, University of Washington
• Wah Chiu — cryo-EM pioneer, Stanford