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Input < 1 of 6 >
On the input page, you submit the protein and define the ligand and pocket properties.
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1. To submit the protein, you can fill the PDB id code or browse your computer to upload a file in PDB format to our server.
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2. If you submit the protein by PDB id code, you can open the protein details from the PDB server by clicking the link "View in PDB". You can use this information to learn about the components of your complex and their description in the PDB file.
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3. To submit the ligand you can enter the ligand's keyword or simply let the server choose the biggest non-protein entity in the file as the ligand, by clicking on "Automatically assign".
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4. The keyword can be any entity found in the file (for example "SER123:A" means that the ligand is located in the residue serine, sequence number 123 in chain A). you can also describe the ligand as a sequence of residues (for example SER123:A-GLY128:A" means that all the residues from 123-128 are considered as the "ligand", or "SER123:A,GLY128:A" for only these two residues.
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5. Define the pocket's size (in Angstroms) and shape
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6. More advanced option are the gap length, terminals, other molecules including and the options to preserve secondary structures in the pocket. |
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