Should I use crystal structure of protein for molecular docking and Is ıt easiest the process ?

More Ergin Karatekin's questions See All

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PCR Sample Purification, what is the difference between KOH and NaOH?

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After purification from agarose gel, DNA concentration cannot be measured in the nanodrop, but can be visualized in the gel. What could be the reason?

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How to I combine 2 ligands to 1 receptor for molecular docking using autodock vina ?

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With which formula can the metabolic energy value of silage be calculated (for chickens, especially geese). Which is the current or most valid method?

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Is it suitable to use a density-based solver to solve supercritical CO2 laminar flow?

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What is your pump manufacturer recommendations, ensuring low flow rate and high operating pressure?

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Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

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How to understand this crystallographic phenomenon of low temperature crystals in zeolite?

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For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

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Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

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Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

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How to start a Molecular Dynamics Simulation?

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Which will be the best software for the Hydration shell analysis with molecular dynamics?

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Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

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How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

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Why Powder XRD is performed after cruhsing a crystal if Single Crystal XRD analysis of the same crystal has been performed already ?

What information we can get from PXRD analysis other than from SCXRD analysis of a crystal ?

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Rushali Haridas Dudure

Yes, you have the x-ray crystal structure of protein for docking .

Muni Sireesha Sunkara

Download it from PDB .

Asadollah Asadi

Yes. Also it is recommended to include solution state and determine charge of ionizable functional groups of residues and ligand.

Mohammed Shamil

draw the ligand by ChemDraw and protein from PDB

Mohammad Taghizadeh

For receptors, crystal structures are in a higher position but if there wasn't a crystal structure a good structural model could be the next option. For ligands, the PubChem ligands could be good choices.