I tried docking same ligand with the same protein prepared from different pdb complex from rcsb page. They yielded different results. that made me wonder which pdb complex of the protein should I select for docking. Autodock vina docking
Select a file with higher resolution and also read the publication attached with it. Search for the number of chains and select one with lesser number of chains. Also this article may be helpful. https://www.researchgate.net/post/For-docking-what-are-the-criteria-to-choose-the-best-protein-structure-from-PDB-to-be-used-as-the-target
Rabeya Bosri Depending on your Interest, check the mutational status of the PDB and the lowest possible resolution
It depends on what kind of docking you are looking forward to do. You can filter your requirements in PDB such as you can filter 'Homo sapiens' if you are looking for a protein involved in humans. Some structures might even have certain compounds such as metal ions or other ligands bound to them (read through the publication attached and select accordingly)
I understand you ask about different chain in protein pdb file. First go through literature and find the chain with ligand. On e thing also consider ligand have similar moity and protein of high resolution..
File download in gz format
key points to be considered would be:
1. Resolution
2. Species
3. Missing Residues
4. co-crystallized ligand
- Badges
- Science method