Include additional data, references

[davidlmobley]

References:

• Read Lindorff-Larsen, Miao papers on lsozyme binding; include references and relevant insights. Lindorff-Larsen reference: https://elifesciences.org/articles/17505
• Reference Pan paper: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00172
• Add Minh/Xie reference on multiple binding modes in L99A (10.1021/acs.jctc.6b01183); this same paper also notes difficulty in converging Yank binding free energy calculations (section 3.3).
• Add additional trypsin references -- Tiwary, De Fabritiis, Noe, Doerr, Buch, Dickson, Amaro

Data curation

• Provide isomeric SMILES for all compounds outside the LaTeX
• Add info on ionization states. Tables typically show 2D structures for neutral forms; files provide a guess. This needs explaining. Suggestion: "Add info to the legends of the tables with the benchmark compounds and data some information about the relationship between what is shown in the table and what is provided in the molecule files. We may state that the molecules files provide a reasonable guess for the ionization states for the free ligands, but it is ultimately up to the user to decide what they want to do about ionization states if they are trying to match experiment."
• Update octa acid uncertainty information (see DLM tasks)
• Clean host/guest files so guest is not multi-residue, and hosts have residue number 1.
• Possibly add Pan/Xu FKBP data/example/inputs, see DLM tasks
• Possibly add lysozyme inputs from Rizzi, see DLM tasks
• Check carboxylic acid bond order problem (?) -- Add CD benchmarks to manuscript #47 (comment)
• Possibly re-generate guest starting structures using docking, Provide bound-state starting structures for hosts #50

Additional discussion/paper editing:

• Discuss hydration free energies and FreeSolv (by request; readers felt this was important to mention)
• Note availability of Minh/Xie curated set of lysozyme binders, which now lives on Mobleylab GitHub
• Clearly delineate soft and hard benchmarks in subsection headers
• Fix typo -- p8, beginning of GDCC section 2, "directly with bound hosts" -> "directly with bound guests"
• Note L99A/M102H as of possible future interest.
• Add Ponder insights from SAMPL7 webinar (available online on Zenodo) to paper -- particularly that changing flexibility around upper ring affects binding of guests by 4-5 kcal/mol (said about 8:34 am) and that the diphenyl ether has two coupled torsions; can’t be fit as a sum of 1D C-O torsions. So they had to use 2D torsion-torsion coupling term (!!).

Other

• License writing under CC-BY since only code can be MIT
• Update eScholarship links to GitHub and vise versa