Add supramolecular benchmark: PLA15

docs/source/user_guide/benchmarks/index.rst

@@ -7,3 +7,4 @@ Benchmarks
 
     surfaces
     nebs
+    supramolecular

docs/source/user_guide/benchmarks/supramolecular.rst

@@ -0,0 +1,53 @@
+==============
+Supramolecular
+==============
+
+PLA15
+======
+
+Summary
+-------
+
+Performance in predicting protein–ligand active-site interaction energies for the
+PLA15 set of 15 complexes. Systems range from 259 to 584 atoms and contain complete
+active sites. Ligands contain 37–95 atoms with net charges of −1, 0, or +1 and all contain
+aromatic heterocycles. Five ligands contain either divalent of tetrahedral sulfur atoms, and
+four and three of them contain F and Cl atoms, respectively.
+
+Metrics
+-------
+
+Total MAE
+
+For each complex, the interaction energy is calculated by taking the difference in energy between the protein-ligand complex and the sum of the individual protein and ligand energies. The MAE is computed by comparing predicted interaction energies to reference interaction energies across all 15 systems.
+
+Pearson's r²
+
+The squared Pearson correlation coefficient between predicted and reference interaction energies, measuring the proportion of variance in the reference values explained by the model predictions.
+
+Ion-Ion MAE
+
+For each complex where both protein and ligand fragments have non-zero charges, the interaction energy error is calculated. This metric reports the MAE for these ion-ion interaction systems.
+
+Ion-Neutral MAE
+
+For each complex where one fragment (protein or ligand) has a non-zero charge and the other is neutral, the interaction energy error is calculated. This metric reports the MAE for these ion-neutral interaction systems.
+
+
+Computational cost
+------------------
+
+low: tests are likely to take minutes to run on CPU.
+
+Data availability
+-----------------
+
+Input structures:
+
+* K. Kříž and J. Řezáč, ‘protein ligand - Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design’, J. Chem. Inf. Model., vol. 60, no. 3, pp. 1453–1460, Mar. 2020, doi: 10.1021/acs.jcim.9b01171.
+* Structures download found in SI
+
+Reference data:
+
+* The Supporting Information also provides the interaction energies.
+    * The benchmark interaction energies are based on a combination of explicitly correlated MP2-F12 calculations and a DLPNO-CCSD(T) correction