Tool:How Study Aromatic-Aromatic Interactions And Amino-Aromatic Interactions Of Protein-Ligands Complexes In The Pdb.

Question

[bagaruwa]

Dear all,

What are the best ways to study aromatic-aromatic interactions and amino-aromatic interactions between protein binding site residues and ligands in the PDB. What are the best free and paid software I can use to do an excellent job.

Thank you,
Dr. Abubakar Abdullahi.

Answer 1

[Jiyao Wang]

You could use iCn3D to get all interactions including aromatics (pi-stacking and pi-cation) in the menu "Analysis > Interactions". One example is at https://structure.ncbi.nlm.nih.gov/icn3d/share.html?CuXYgGLCukDeUKnJ6

Answer 2

[Vladimir Chupakhin]

Software and databases from CCDC can perfectly do this job, but it's paid. Also interaction fingerprints (IFP) can encode the aromatic interactions between protein and ligand: PLIF - opensource IFP library, honestly don't know if the aromatic interaction is included in it. FingerPrintLib - by Didier Rognan Lab, - can definitely do fingerprint calculation with detection of aromatic interaction (two types).

PS: Actually there are tons of literature about aromatic interaction of the amino acids and ligands in protein-ligand complexes.