The problem of computational affinity estimation has grown as
computers became a powerful tool of today science. It is hardly to find
any modern investigation that is not aided with computational models.
However demands of scientists expand even faster than microelectronic
industry capabilities. Numerous computational clusters help to facilitate
bio- and pharmacological projects. Nevertheless the numbers of projects
that require rigorous computations are growing. To deal with this
problem researches worldwide have to use in their projects less accurate
but computationally faster theoretical methods. That is why new, more
efficient and faster algorithms are of great importance in modern
Mathematical modeling in biology is a problem often related to
interactions estimation between a biomolecular target and small molecule
compounds. The knowledge of such interactions permits us to interrupt
certain processes in cells and, for example, to impede such a devastating
disease as cancer. For this reason a lot of efforts are concentrated on
designing of better models and algorithms for high-throughput virtual
One of the leading Ukrainian companies, OTAVA Ltd., started
developing its own virtual screening system in 2004 [1-3]. The project
was started as an attempt to incorporate entropy change that occurs
during ligand-receptor binding into virtual screening protocol. Initially
this project was restricted to model entropy change in harmonic
oscillation approximation. As such model is extremely related to quality
of potential energy calculations. OTAVA’s scientists have designed a
universal polarizable 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 showed some lack in accuracy. It was significantly
improved with addition of ligands desolvation free energy which was
calculated with our modified GBSA method (up to 0.95 regression
coefficient with experimentally derived data).
Further testing of the improved virtual screening system showed
strong dependence of its efficiency on nearest environmental water
molecules that are usually ignored in the field of high-throughput virtual
screening. To implement fast but accurate water position finding, a new
algorithm of molecular docking code was proposed by OTAVA’ scientists
and its utilization is on the way in our laboratories.
List of selected publications by OTAVA’s scientists:
 O.Ya. Yakovenko, A.A. Oliferenko, V.G. Bdzhola, V.A. Palyulin,
N.S. Zefirov. Kirchhoff atomic charges fitted to multipole
moments: implementation for a virtual screening system. J.
Comput. Chem. 2008, 29, 1332.
 Yakovenko O.Ya., Olifirenko A.A., Golub A.G, Bdzhola V.G.,
Yarmoluk S.M. The new method of distribution integrals
evaluationsfor high throughput virtual screening. Ukrainica
Bioorganica Acta - 2007. – Vol. 5, No. 1. – P. 52-62.
 Yakovenko O.Ya., Golub A.G., Bdzhola V.G., Yarmoluk S.M.
Application of distribution function of rotation and
transla_tion degrees of freedom for CK2 inhibitors Ki