User: Karim Afifi

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Posts by Karim Afifi

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(Closed) Inquiry about masters degrees?
... I have just had my BSc in Computer Science and I am looking to inquire about which field I should pursue in completing my masters degree. My graduation project was related to protein docking. I analyzed different approaches to improve the performance of scoring functions by using different technique ...
computation chemistry drug design biophysics written 18 months ago by Karim Afifi0
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How to calculate the in-ring torsion angle?
... How to calculate the in-ring torsion angle for a ring of size 5 or 6 from a pdb file? ...
angle ring pdb written 22 months ago by Karim Afifi0
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How to determine hybridization states for a protein pdb file format?
... How can I determine hybridization state and bond order for all atoms in a protein pdb file? In general, how can I acquire the same information for a pdb file as a mol2 file format? Multiple research papers state that for proteins, bond orders can be easily deduced but for a ligand, it is not easy. I ...
pdb protein docking written 22 months ago by Karim Afifi0
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pdbbind and mol2 to pdbqt
... what are the steps necessary to prepare a protein and a ligand for docking using autodock vina? ...
autodock written 2.1 years ago by Karim Afifi0

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