Info
The wwPDB/CCDC/D3R Ligand Validation Workshop was convened in July 2015 to define community standards for validating small-molecule ligands in macromolecular crystal structures. The 2016 output paper - Adams et al., “Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop,” Structure 24(4):502-508 (2016) - brought together the wwPDB core archives, Cambridge Crystallographic Data Centre (CCDC), Drug Design Data Resource (D3R), software vendors, PHENIX/CCP4 developers, academic crystallographers, and a broad pharmaceutical industry cohort. This was an unusually wide cross-section of the X-ray ligand ecosystem and makes the workshop an excellent “who knows whom” node.
Workshop co-organizers
| Organizer | Role / Affiliation |
|---|---|
| Stephen K. Burley | Director, RCSB PDB |
| Victoria Feher | Project Scientist, D3R, UC San Diego |
| Colin Groom | Executive Director, CCDC |
| Gerard Kleywegt | Head, PDBe |
| John Markley | Founding Head, BMRB |
| Haruki Nakamura | Founding Head, PDBj |
| Anthony Nicholls | President and CEO, OpenEye Scientific |
2016 paper participants (55 total)
wwPDB archive teams
Software developers and academic crystallographers
| Participant | Affiliation |
|---|---|
| Paul Adams | Lawrence Berkeley National Laboratory |
| Thomas Terwilliger | Los Alamos National Laboratory |
| Paul Emsley | MRC Laboratory of Molecular Biology |
| Garib Murshudov | MRC Laboratory of Molecular Biology |
| Randy Read | University of Cambridge |
| Gerard Bricogne | Global Phasing Ltd |
| Wladek Minor | University of Virginia |
| Andrzej Joachimiak | APS / Argonne National Laboratory |
| David Case | Rutgers |
| Joseph Marcotrigiano | Rutgers CABM |
| Gaetano Montelione | Rutgers |
| Alan Mark | University of Queensland |
| Dale Tronrud | Oregon State University |
Small-molecule / chemoinformatics
| Participant | Affiliation |
|---|---|
| Colin Groom | CCDC |
| Suzanna Ward | CCDC |
| Victoria Feher | Drug Design Data Resource, UC San Diego |
| Evan Bolton | NCBI / NLM |
| Marc Nicklaus | NCI / NIH |
| Talapady Bhat | NIST |
| Radka Svobodova | CEITEC Masaryk University |
| Tobias Krojer | Structural Genomics Consortium Oxford |
| Wolfram Tempel | Structural Genomics Consortium Toronto |
Software / tooling industry
| Participant | Affiliation |
|---|---|
| Anthony Nicholls | OpenEye Scientific |
| Tom Darden | OpenEye Scientific |
| Gregory Warren | OpenEye Scientific |
| Jeffrey Bell | Schrödinger |
| Thomas Holder | Schrödinger |
| Cary Bauer | Bruker AXS |
| Pamela Williams | Astex Pharmaceuticals |
Pharma industry
| Participant | Affiliation |
|---|---|
| Kirk L. Clark | Novartis Institutes for BioMedical Research |
| Kathleen Aertgeerts | DART NeuroScience |
| Jeff Blaney | Genentech |
| Seth Harris | Genentech |
| David Brown | University of Kent / Charles River |
| Jorg Hendle | Lilly Biotechnology Center |
| Anil Padyana | Agios Pharmaceuticals |
| Catherine Peishoff | Bristol-Myers Squibb |
| Susan Pieniazek | Bristol-Myers Squibb |
| Steven Sheriff | Bristol-Myers Squibb |
| Stephen Soisson | Merck Research Laboratories |
| John Spurlino | Janssen Pharmaceuticals |
| Robert Nolte | GlaxoSmithKline |
| Terry Stouch | Science For Solutions, LLC |
Primary source
- Adams et al., “Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop,” Structure 24(4):502-508 (2016): https://www.cell.com/structure/fulltext/S0969-2126(16)00076-9