×This is not a valid ArchDB classification code.
If you are not familiar with ArchDB codes (such as DS.HE.1.1.1) we recomend you to use the database browser.
×ArchDB 2014: structural classification of loops in proteins. Jaume Bonet, Joan Planas-Iglesias, Javier Garcia-Garcia, Manuel A. Marín-López, Narcis Fernandez-Fuentes and Baldo Oliva Nucl. Acids Res. (2014) doi: 10.1093/nar/gkt1189 |
PMID: 24265221
Download
For users that want to work locally with ArchDB's classification, we offer the option to download a tabulated file with ArchDB's main data or compressed SQL content.
The downloadable data does not contain external database assignations such as the SCOP relations that can be otherwise found by browsing through this site.
Take into acount that loops with more than one classification will appear once for each classification to which they belong.
The fields of the downloadable file can be defined as follows:
loop_id: This is the unique code by which a loop is identified.
How can I use it?
pdb: Original structure file from which the loop was identified.
chain: Original structure chain from which the loop was identified.
start: First position of the loop in the protein chain.
end: Last position of the loop in the protein chain.
type: Type of the bracing secondary structures.
length: Number of amino acids in the aperiodic structure region.
NtermLength: Length of the N-terminal secondary structure.
CtermLength: Length of the C-terminal secondary structure.
distance: The euclidian distance between the boundaries of the aperiodic structure.
theta: The angle between M1 and M2.
rho: The angle between M2 and the plane Γ defined by the vector M1 and the normal to the plane formed by M1 and D.
delta: The angle between M1 and D.
sequence: Amino Acid sequence of the loop
secondary_structure: Secondary structure of the loop
exposition: Evaluation of the exposition of the loop
ramachandran: Consensus ramachandran of the class the loop has been classified to (if any)
This field can be NULL in the case of non-classified loops
classification: Identifier of the subclass the loop has been classified to.
How can I use it?
This field can be NULL in the case of non-classified loops
loop_id permalink
You can get more information from the loop by adding the loop_id at the end of our permalink or copying it and doing it manually (recomended if querying for several loops)
A loop_id code has a format like: AAAA_B_123 where the first 4 letters correspond to the PDB code, the second section to the chain and the last one to the first position of the loop (can include negative sign and letters).
It looks like this loop_id does not correspond with any loop in our database. Please check your search.
ArchDB subclass permalink
You can get more information from the subclass by adding the classification at the end of our permalink or copying it and doing it manually (recomended if querying for several classes or subclasses)
A subclass code has a format like: MM.TT.1.1.1 where MM refers to the clustering algorithm, TT to the type, the first number to the length and the following numbers to class and subclass respectively.
It looks like this subclass does not correspond with any subclass in our database. Please check your search.