VVTAK Connecting Bridges
Download VVTAK Connecting Bridges
This algorithm is for prediction of the most probable conformational state (pure coil [C] or coil with 3/10 helix [I]) of the "connecting bridge" between two "major" elements of secondary structure (alpha helices [H] and/or beta strands [B]).
The algorithm works with FASTA amino acid sequences from www.pdb.org and the text from PDB file (it can be opened by any text viewer).
1. Enter amino acid sequence in FASTA format (the one from www.pdb.org site) in the designated line of "Sequence" list. Don't forget to delete all the lines left from the previous protein.
2. Enter the whole text from PDB file into the "PDB" list. Don't forget to delete all the lines left from the previous protein.
On the "OUTPUT" list one will see the table containing 5 columns:
i) number of amino acid residue,
ii) amino acid residue (in one letter code),
iii) 3/10 helices boarders according to the PDB file (designated by "I" letter),
iv) connecting bridges according to PDB file (designated by either "I" or "C" letter),
v) preferable conformational state of connecting bridges (designated by either "I" or "C" letter).
All the probability scales can be found in the "Scales" list.