Comments (5)
That sounds good, and it can be done quickly I think. I'll change the ligands names to a provided ID (from 1 -10), and change the associated tables in the paper and in the README file.
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Working in the BRD4(1) benchmarks table in the main paper, and I won't fit in the page if I keep the ligand names but also add an extra ligand ID column (as done in the CD tables). Should I drop the ligands names altogether? They might not be essential since we are also providing the references.
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I'm all for dropping the ligand names, or if you really want to keep track of them, put them in footnotes or in a separate markdown file you link to.
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No we can drop them, I only gave the ligands names so the table would look the same as the Lysozyme one. I'll just give a number for each, which will also make the table look better (it was a little decentralized before since it was too wide). Then I'll change the README table and the ligand files names.
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Resolved for bromodomains in #48 ; still needs to be done for lysozyme.
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Related Issues (20)
- Add README.md for host-guest inputs; add additional info
- Update text to reflect host-guest sets added in #22 HOT 1
- CD mol2 files coordinates starting in the binding pocket HOT 20
- Add additional supplementary data, perhaps in markdown files? HOT 5
- Get CD benchmarks in? HOT 3
- Provide suitable README files for CB7, GDCC benchmarks
- Provide bound-state starting structures for hosts HOT 5
- Deposit calculated values for provided files when available HOT 5
- Should we use table titles and not numbers in markdown files? HOT 6
- Parmed bug affecting cyclodextrin files HOT 6
- Update README.md to reflect how to cite (once discussion is final) HOT 4
- Mixed 1-4 scaling? HOT 2
- Typo in reference for Lysozyme L99A/M102Q - catechol experimental value? HOT 3
- Errors using cyclic host `mol2` files with non-unique atom names HOT 11
- Add machine-readable tables for all the sets HOT 3
- The SDF files for charged compounds aren't listing the formal charges of the atoms HOT 2
- PDB files for BRD4 parameterized systems are missing CONECT records HOT 2
- Include additional data, references
- gdcc-set2 and CB experimental Delta H is missing HOT 4
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