Table 1.
Summary of the facilities mentioned in this article
| Facility | Short description |
|---|---|
| wwPDB1 | Worldwide PDB. Macromolecular data collection and distribution. |
| UniProta , 12 | Worldwide collection of protein sequences |
| Swiss‐Protb | Manually annotated and reviewed section of the UniProt |
| PDB‐REDO10, 13 (improved) | Reanalyzed, consistently treated structure models |
| BDB14 | PDB entries with standardized, isotropic B factors |
| DSSP5 (improved) | Secondary structure assignment for protein structure models |
| DSSP_REDO (novel) | Like DSSP, but for PDB‐REDO entries |
| WHAT IF6 | Protein structure calculations. Outdated; some useful aspects as servers. |
| YASARA_Viewc | Free (feature‐rich) molecular viewer that additionally contains all of WHAT IF |
| HSSP8 | Multiple sequence alignments against UniProt for proteins in PDB. |
| VASEd (novel) | Visualization of entropy/variability values in HSSP entries |
| PDB‐Vise (novel) | Visualization of crystal packing contacts, and a few more things |
| LigPlotf | 2D representation of ligand–macromolecule interactions |
| Lists (partly novel) | Sets of precalculated data for all PDB entries (see Table 3) |
| PDB_REPORT15 (improved) | Reports (in a PDF format) about anomalies and errors in PDB entries |
| WHY_NOTg | System that explains why certain data files are not present |
| pdbadh | Anecdotal list of problems in PDB entries |
| PDBFINDER | Easy to parse PDB metadata |
| PDBsumi | Summary of PDB metadata useful for PSB |
| LigPlotj | Visualizes interactions between macromolecules and ligands16 |
| PDB_SELECT | Subsets of PDB entries (sequence unique at 30% cutoff) |
| PISCESk | More extensive system for making sequence unique subsets of PDB entries |
| CATHl, SCOPm, DALIn | Three facilities that shed light on the 3D relations between PDB entries |
| Swiss‐Modelo | Builds homology models |
| Sternbergp Brunakq | Examples of long‐time stable group pages with many useful facilities |
Notes: The facilities in blue are produced by the authors of this article; the facilities in black are produced and maintained by others and we believe them to be useful for users of our facilities. Most of our facilities can be downloaded from ftp://ftp.cmbi.umcn.nl/pub/molbio/data/ and the software from the cmbi section in GitHub. YASARA_View can be downloaded freely from http://www.yasara.org/. http://swift.cmbi.umcn.nl/gv/facilities/ provides extensive documentation for the databases and instructions for obtaining an in‐house copy via rsync. Facilities without reference have not been published explicitly yet. References to some facilities are best extracted from those facilities' web pages. The facilities that are published here for the first time are labeled with the word “novel”. Facilities that underwent major updates since they were last published are labeled with the word “improved.”