I docked the GOLD program version 5.7.2 and when analyzing the interactions between the ligand and the receptor I noticed that the amino acid sequence is incorrect when saving the complex in pdb. Any suggestions to solve this problem?
Many protein structure viewers will allow the renumbering of aminoacids. You can fix the first amino acid in structure to any other number and then all subsequent residues will be renumbered.
Hello Carlos Serrão
Actually, whenever you remove any residue or change the actual sequence in a pdb file or especially at instances, when you dock two different protein structures, there are chances for the formation of overlapping numbers. This issue can be rectified using simple online renumbering servers, where all the constituents of your multiple chains get sequentially numbered, thereby prevents number overlapping.
The link for an online renumbering tool is given below:
https://swift.cmbi.umcn.nl/servers/html/renumb.html
This response has also been recorded by me in a similar question, whose link is given below:
https://www.researchgate.net/post/Why_am_I_getting_an_error_using_HADDOCK_web_server_for_docking_studies
Hope it helps.
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