Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: A major uncertainty in binding free energy estimates for protein–ligand complexes by methods such as MM-PB(GB)SA or docking scores results from neglecting or approximating changes in the configurational entropies (ΔSconfig.) of the solutes. In MM/PB(GB)SA-type calculations, ΔSconfig. has usually been estimated in the rigid rotor, harmonic oscillator approximation. Here,  present the development of a computationally efficient method (termed BEERT) to approximate ΔSconfig. in terms of the reduction in translational and rotational freedom of the ligand upon protein–ligand binding (ΔSR/T), starting from the flexible molecule approach.  test the method successfully in binding affinity computations in connection with MM-PBSA effective energies describing changes in gas-phase interactions and solvation free energies. Compared to related work by Ruvinsky and co-workers, clustering bound ligand poses based on interactions with the protein rather than structural similarity of the poses, and an appropriate avera...
['Ido Y. Ben-Shalom', 'Stefania Pfeiffer-Marek', 'Karl-Heinz Baringhaus', 'Holger Gohlke']
I am writing a research paper on a idea Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
[{"from": "human", "value": "I am writing a research paper on a idea Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: A major uncertainty in binding free energy estimates for protein\u2013ligand complexes by methods such as MM-PB(GB)SA or docking scores results from neglecting or approximating changes in the configurational entropies (\u0394Sconfig.) of the solutes. In MM/PB(GB)SA-type calculations, \u0394Sconfig. has usually been estimated in the rigid rotor, harmonic oscillator approximation. Here,  present the development of a computationally efficient method (termed BEERT) to approximate \u0394Sconfig. in terms of the reduction in translational and rotational freedom of the ligand upon protein\u2013ligand binding (\u0394SR/T), starting from the flexible molecule approach.  test the method successfully in binding affinity computations in connection with MM-PBSA effective energies describing changes in gas-phase interactions and solvation free energies. Compared to related work by Ruvinsky and co-workers, clustering bound ligand poses based on interactions with the protein rather than structural similarity of the poses, and an appropriate avera..."}]