The Katchalski-Katzir algorithm is an algorithm for docking of rigid molecules, developed by Ephraim Katchalski-Katzir, Isaac Shariv and Miriam Eisenstein. In 1990 Professor Ephraim Katchalski-Katzir, former president of the state of Israel, gathered a group of physicists, chemists and biologists at the

Weizmann Institute of Science The Weizmann Institute of Science ( he, מכון ויצמן למדע ''Machon Vaitzman LeMada'') is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli univ ...

, to discuss intermolecular recognition. One of the outcomes of these discussions was the Katchalski-Katzir Algorithm, proposed by Dr. Isaac Shariv, a physics PhD student at the time. The Algorithm was implemented in a computer program, MolFit, by Dr. Miriam Eisenstein from the department of Structural Chemistry. It is a purely geometric algorithm, but some extensions of it also implement

electrostatics Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for am ...

. The algorithm's first step is mapping the molecules onto grids, with each point of a grid being marked as either: * outside the molecule * on the molecule's surface * inside the molecule The algorithm increases the surface contact and minimizes volume overlap. It is straightforward to compute such a score for a single alignment, but there are too many possible ways to align the molecules to simply iterate over them all. To compute the scores for many alignments efficiently,

fast Fourier transform A fast Fourier transform (FFT) is an algorithm that computes the discrete Fourier transform (DFT) of a sequence, or its inverse (IDFT). Fourier analysis converts a signal from its original domain (often time or space) to a representation in t ...

(FFT) is applied to both grids. Having the grids in FFT form lets the scoring to be computed for many different alignments very quickly. The Katchalski-Katzir algorithm is a fast but rather limited algorithm. It is usually used to quickly filter out the obviously wrong candidate structures. A structure may have good Katchalski-Katzir score (that is, fits well geometrically), but be a very bad fit overall, for example due to unfavourable

electrostatic Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for am ...

interactions or

hydrophobic In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, ...

and

hydrophilic A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press. In contrast, hydrophobes are ...

groups facing each other. This is not a serious problem, as such structures can be filtered out later. A bigger issue is when a favourable structure is rejected by the algorithm. Some cases where this may happen include bad geometric fit being overcome by very strong attractive forces, or where the shape of the target changes because of the interactions (

induced fit Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, calle ...

). Programs that implement the Katchalski-Katzir algorithm include MolFit and FTDock.

References

{{Reflist Molecular modelling Computational chemistry Geometric algorithms

See also

References