Good morning, Dear Professor,

My name is Zhenjiao Du, from Kansas State University.

I am employing molecular docking for peptide screening and need to build peptide ligands for docking screening. I used to generate ligand by VMD and then energy minimized by molecular dynamics simulation, but the final conformation is not that matchable to the crystallography results. Chimera generated ligands perform a better job.

I find Chimera provides amazing ligand energy minimization protocols, but there is no any resource for the scripts based ligand generation and minimization since I might need to generate thousands of peptide ligands for virtual screening. I find Chimera also supports python programming.

Could you please provide me some information for the ligand generation by Chimera based on python scripts? I really appreciate it.

I am looking forward to your reply.

Sincerely,

Zhenjiao Du

Vice president of CAFS Student Committee

Ph.D. student, Cereal Chemistry

Grain Science & Industry, Kansas State University

150A Waters Hall, Manhattan, KS 66502

Pronouns: He/His