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Simbiome is a curated, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences.
Kinemage Protein Structures
500 proteins used for the Ramachandran-plot distributions, with File ID {PDB code + chainID}
http://kinemage.biochem.duke.edu/databases/top500.php
| Database or Data Source | |
This a list of 500 proteins used for the Ramachandran-plot distributions, with File ID {PDB code + chainID (if not the full PDB file) + H (to signify H`s added), structure factor deposition status, resolution, and protein name. The filters used to choose them were: resolution 1.8 _A_ or better, clashscore (for atoms B<40) < 22/1000atoms (see Word et al. 1999, J. Mol. Biol. 285, 1709 for clashscore definition), fewer than 10/1000atoms whose mainchain bond angles (incl to Cbeta) are >5 std deviations from Engh & Huber geometry (1991, Acta Cryst A 47, 392), no unusual amino acids with mainchain substitutions (e.g., 1mroA, 1rtu), no free-atom refinements (e.g., 1nxb), wildtype preferred to mutant if otherwise approximately equivalent, and if proteins related but not same, took best combination of resolution and clashscore. | |
| Development Stage | 4 - Development with public userbase |
| Keywords | |
| Size Scale | 1 - Atomic / Molecular |
| Resources with Similar Function | |
| Related Resources | PDB - Protein Databank Search Google |
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This work is licensed under a Creative Commons Attribution 2.5 License.