rmoretti Staff Lv 1
Objectives
Objectives in this puzzle are driven primarily by the evaluation criteria used by CACHE.
Maximum bonus: +12 000
Similarity (max +1000)
Gives a bonus if the current compound is "similar enough" to the starting (hit) compound. The "percent similarity" being calculated is not quite linear from a visual perspective (search for Tanimoto Similarity for further discussion), and is different from the similarity value being calculated for the Compound Library.
Ligand Identity (max +1000)
In this puzzle series, we're looking for novel ligands. The Ligand Identity objective will give a bonus if you make a ligand which is different from the starting ligand.
Compound Library (max +1000)
Gives a bonus if your current compound is in the library. This uses a local cached version of the Compound Library search results to determine if the compound is in the library. If you manually create a compound that happens to be in the library (or if you load a shared solution with an on-library compound), you may need to submit the compound to the compound library search and wait to get the results back before the objective can properly recognize that the compound is in the library. (If the objective is not updating, try wiggling the structure. See this forum post for more discussion.)
Acid groups (max +1000)
Certain groups like carboxylate and phosphate would make compounds not ideal for drug usage. This gives a bonus if the compound is missing these problematic groups. (Show highlights regions of the molecule at issue.)
Torsion Quality (max +1000)
Keeps bond rotations in a good range. Using Wiggle or Tweak Ligand can fix bad torsions. (Show highlights torsions to be rotated.)
Number of Rotatable Bonds (max +1000)
Intended to keep the ligand from getting too big and floppy. You can reduce rotatable bonds by deleting groups or forming rings. (Show highlights rotatable bonds.)
Ligand TPSA (max +1000)
Topological Polar Surface Area - Keeps the polar surface area (including buried polar surface) low. To improve, try removing oxygens and nitrogens. (Show highlights atoms contributing to higher TPSA.)
Ligand cLogP (max +1000)
A measure of polarity - Keeps the molecule from getting too hydrophobic. To improve, try adding polar oxygens and nitrogens. (Show highlights atoms contributing to higher cLogP.)
Fraction of four-bonded carbons (max +1000)
Measures how carbons with bonds to four atoms ("sp3 hybridized") there are. Too few (too many double and triple bonded carbons) is bad. (Show highlights carbon atoms at issue.)
Bad Groups (max +1000)
Gives a bonus for avoiding groups that interfere with assays, or which are far from the compounds in the library. (Show highlights groups at issue.)
Molecular Weight (max +1000)
Keeps the ligand a reasonable size.
Synthetic Accessibility (max +1000)
Keeps the ligand from going too far from the compounds in the library. (Show highlights parts of the molecule at issue.)
