The Protein Coil Library: The Derived Unordered Fragment Library

Welcome to the Protein Coil Library!

This is the website for The Protein Coil Library, a library of protein structure fragments derived from the Protein Data Bank (PDB). The fragments in this library are those fragments in the PDB that cannot be classified as either alpha-helix or beta-strand. Three-dimensional structures as well as side-chain and backbone torsion angles are stored in the database.

The library stores the complete torsion angle descriptions for the fragments as well as the three dimensional structures of the fragments themselves. The goal of extracting and pre-calculating this data is to allow for more straightforward investigation of peptide structure without the background of secondary structure elements.

In addition to searching by PDB ID, it is possible to download a particular size class, perform a batch search of PDB/chain ID's, or download precompiled lists of PDB ID's of interest (PDB Select, etc.). For users interested in browsing the entire database at once or maintaining their own locally-updated copy of the library, FTP access instructions are also provided.

The concept of a coil fragment library was originally motivated in Swindells, M. B., MacArthur, M. W., and Thornton, J. M. "Intrinsic φ, ψ propensities of amino acids, derived from the coil regions of known structures." Nat. Struct. Biol. 2 (1995): 596-603. Details on the generation of the library, as well as references to other papers are given in the methods section. Some analysis utilities and details on the file organization of this implentation are available, as is a description of the file formats used here.

If you have other questions regarding the coil library, please feel free to contact the maintainers. We will try to respond as quickly as possible. Finally, if you would like to use this implementation in your own research, please cite:

Fitzkee, N. C., Fleming, P. J, Rose G. D. (2005) Proteins. 58 (4): 852-4.

Important Note: The Protein Coil Library was created in 2005, and the field of structural biology has advanced significantly since then. While this site remains functional, we have not implemented new features of the wwPDB. Importantly. the coil library knows nothing about mmCIF files, and therefore some larger structures (especially those generated using cryo-EM) will be absent from this site. We apologize for the inconvenience! (Nick Fitzkee, December 23, 2022)

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