Modern drug development relies on understanding the interaction of proteins and ligands. In many protein-ligand systems, the affinity of a protein for a ligand is quantified in the systems free binding energy, ΔG. This project describes the development of an automated workflow for the coarse-grained lattice method for predicting free binding energies in protein-ligand systems previously developed and tested on Zn(II)-protein systems. The workflow was developed and tested with the original Zn(II)-protein system to ensure accuracy. It was subsequently used to extend this method to Cu(I)-protein systems. The new workflow improves the efficiency of extending this method to different metal-protein systems.

• This report represents the work of one or more WPI undergraduate students submitted to the faculty as evidence of completion of a degree requirement. WPI routinely publishes these reports on its website without editorial or peer review.

Creator

• Aronoff, Jonathan

Publisher

• Worcester Polytechnic Institute

Identifier

• E-project-042723-165123
• 106641

Keyword

• computatoinal chemistry
• free energy
• metal protein
• lattice
• coarse-grain
• protein-ligand binding

Advisor

• Neamtu, Rodica
• Kaminski, George A.
• Heilman, Destin
• Mortensen, Jennifer

Year

• 2023

Date created

• 2023-04-27

Resource type

• Major Qualifying Project

Major

• Biochemistry

Source

• E-project-042723-165123

Rights statement

• In Copyright

Last modified

• 2023-06-14