Table 3.
Protein-ligand validation software
| Validation | Package | Description | URL | Reference |
|---|---|---|---|---|
| Quality and fit of ligand | Twilight | Visual analysis of ligand density | http://bit.ly/1shcwu4 | [12, 15] |
| VHELIBS | Fit of ligands and binding sites | http://bit.ly/1t5szxl | [14] | |
| ValLigURL server | Compare conformations of ligands in the PDB | http://bit.ly/1v80yoS | [13] | |
| MotiveValidator and ValidatorDB | Interactive web-based validation of ligands and residues | http://bit.ly/1tNd7Vs | [70] | |
| PDB_REDO | Updated and optimised X-ray structure models and maps | http://bit.ly/1pVYQQA | [21, 22] | |
| wwPDB | wwPDB Validation Server | http://bit.ly/1xdfoZN and http://bit.ly/1si1ZeL | [45] | |
| PDB-CARE and CARP | Checks glycan nomenclature and stereochemistry | http://bit.ly/1pW9gQ0 | [97, 98] | |
| LIGPLOT | Ligand–protein interaction diagrams | http://bit.ly/1qwZ7cS | [85] | |
| EDS | Electron density server | http://bit.ly/1Ddnlkg | [20] | |
| EDSTATS | Statistical quality indicators of electron density maps | N/A | [40] | |
| OVERLAPMAP | Average of two maps | http://bit.ly/ZZUSk3 | [99] | |
| BUSTER | Refinement of proteins and ligands | http://bit.ly/1w8NX1Q | [100] | |
| WHAT_IF/WHAT_CHECK | Protein and ligand verification tools | http://bit.ly/1F0j19Y | [55, 101] |
Software that is particularly useful for ligand validation is highlighted. For general protein structure validation software see Table 4