On analytical corrections for restraints in absolute binding free energy calculations

22 December 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Alchemical absolute binding free energy simulations require an intermediate state at which the ligand is held solely by restraints in a position and orientation resembling the bound state. One possible choice consists of one distance, two angle and three dihedral angle restraints. Here, I demonstrate that in practically all cases, the analytical correction derived under the rigid rotator harmonic oscillator approximation is sufficient to account for the free energy of the restraint.

Keywords

binding free energy
restraint
analytical correction

Supplementary materials

Title
Description
Actions
Title
Additional derivations and technical descriptions
Description
The PDF document (i) summarizes the expressions by Chen et al. [Chen2023] and lists the Mathematica commands by which they can be obtained, (ii) provides some hints on how to obtain the numerical results listed in Table 1 and to reproduce the results by Boresch et al. [Boresch2003], and (iii) outlines how to evaluate the configurational integral for the angle restraint exactly.
Actions

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.
Comment number 1, Stefan Boresch: Dec 22, 2023, 09:31

Please watch for the revised version which should appear within the next 24-48 hours. By my mistake, this version still contains "TO-DO-reminders" to myself which should have been deleted.