Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The adequate choice of the docking target function impacts the accuracy of the ligand positioning as ll as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function  compared positions of its minima with the experimentally known pose of the ligand in the protein active site.  evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources re used. Protein-ligand binding energies calculated using low-energy minima re compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method.
['I. V. Oferkin', 'E. V. Katkova', 'Alexey V. Sulimov', 'Danil C. Kutov', 'Sergey I. Sobolev', 'Vladimir Voevodin', 'Vladimir B. Sulimov']
I am writing a research paper on a idea Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima
[{"from": "human", "value": "I am writing a research paper on a idea Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: The adequate choice of the docking target function impacts the accuracy of the ligand positioning as ll as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function  compared positions of its minima with the experimentally known pose of the ligand in the protein active site.  evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources re used. Protein-ligand binding energies calculated using low-energy minima re compared with experimental values. It was demonstrated that the docking target function on the base of the MMFF94 force field in vacuo can be used for discovery of native or near native ligand positions by finding the low-energy local minima spectrum of the target function. The importance of solute-solvent interaction for the correct ligand positioning is demonstrated. It is shown that docking accuracy can be improved by replacement of the MMFF94 force field by the new semiempirical quantum-chemical PM7 method."}]