Fast and efficient algorithms are important in modern bioscience.
Mathematical modelling in biology is often a problem with interactions estimation between a biomolecular target and small molecule compounds.
Knowledge of this interaction allows the interruption of certain processes in cells, for example it can impede diseases such as cancer.
This is why so many efforts focus on designing better models and algorithms for high-throughput virtual screening techniques.
Otava began developing its own virtual screening system in 2004 to incorporate entropy change that occurs during ligand-receptor binding into virtual screening protocol.
This project was initially restricted to model entropy change in harmonic oscillation approximation.
This model is closely related to quality of potential energy calculations.
Otava's scientists designed a universal polarisable force field to achieve reasonable entropy change accounting (on the basis of unique empirical charges definition scheme).
Spanning entropies with traditional enthalpy calculations for free energy of binding prediction was inaccurate.
Adding ligands desolvation free energy that was calculated with modified GBSA method (up to 0.95 regression coefficient with experimentally derived data) improved the accuracy.
Further testing of the improved virtual screening system showed its efficiency depended on the nearest environmental water molecules, which are usually ignored in high-throughput virtual screening.
Otava's scientists proposed a new algorithm of molecular docking code to implement fast and accurate water position finding.
