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The host-guest component of SAMPL5 is based on two octa-acids, OAMe and OAH, both with the same set of six guest molecules; and one cucurbituril-derived molecular clip, CBClip, with a separate set of 10 guest molecules. Thus, there are three separate datasets, one for each of the three host molecules, and we ask that you submit a separate prediction file for each dataset. The experimental data for OAMe and OAH were obtained by calorimetry, and therefore comprise binding free energies and enthalpies; the experimental data for CBClip were obtained by NMR spectroscopy at a single temperature, and therefore comprise only binding free energies.
A prediction file is a plain text file which contains both your predictions, with uncertainty estimates, and information about your computational protocol. The format requirements for these files are detailed below, and sample files are available for download from the D3R website: OAH-anytexthere-1.txt, OAMe-anytexthere-1.txt, CBClip-anytexthere-1.txt.
Note that you are free to submit multiple predictions, generated by different computational methods, for a given dataset.
If you registered as “anonymous”, please note that the file names and files you submit are subject to public release, so you may want to avoid including identifying information in them.
The name of a prediction file must begin with the name of the host molecule for which it contains predictions (i.e., OAMe, OAH or CBClip, case-independently), and must end with an integer indicating which of your predictions for this host it contains. For example, if you want to submit one prediction file for CBClip, you might name it CBClip-myname-1.csv, where myname is arbitrary text of your choice. If you submit two prediction files for CBClip, you might name them CBClip-myname-1.txt and CBClip-myname-2.txt.
The file will be machine parsed, so correct formatting is essential.
Lines beginning with a hash-tag (#) may be included as comments. These and blank lines will be ignored.
The file must contain the following four components in the following order: your predictions, a name for your computational protocol, a list of the major software packages used, and a long-form methods description. Each of these components must begin with a line containing only the corresponding keyword: Predictions:, Name:, Software:, and Method:, as illustrated in the example files. Each of the four components is now described.
Each non-commented, nonblank line in this component should contain up to the following seven items, separated by commas:
Every line should have six commas, even if you omit some of the optional quantities.
If you computed relative binding free energies, then list free energies referenced to the first guest in the list, and assign guest 1 a binding free energy of 0.0 kcal/mol. This selection is entirely arbitrary and will not affect how your results are compared with experiment.
The name of the protocol should be brief but informative, as illustrated in the example files. Ideally, it will say something about the nature of the method and the key parameters or settings, such as force field chosen or quantum chemistry level.
List the name and version number of each major software package used in your protocol, one package per line.
Please provide a long-form description of the computational method used to make the predictions in this file. The level of detail should be at least as complete as that of a typical “Computational Details” section of a computational paper. Thus, for a simulation-based method, it should describe the sampling methodology and extent, the force field(s) used, the method used to extract thermodynamic results from the predictions (e.g., computational alchemy or double-decoupling for free energies; van’t Hoff or single-box direct for enthalpies), and how statistical uncertainties were evaluated (e.g., statistical inefficiency or blocking analysis)
If you are using MD with explicit solvent to compute binding affinities, you have, hopefully, applied your technology to the two standard setups, for OAH with guests G3 and G4. To submit your results for these special cases, please create a prediction file whose name begins with HGStandard, such as HGStandard-myname.txt. This file should be structured as detailed above, but should only include two prediction lines, for G3 and G4, respectively.