History
In the 1970s, complex modelling revolved around manually identifying features on the surfaces of the interactors, and interpreting the consequences for binding, function and activity; any computer programmes were typically used at the end of the modelling process, to discriminate between the relatively few configurations which remained after all the heuristic constraints had been imposed. The first use of computers was in a study on hemoglobin interaction in sickle-cell fibres. This was followed in 1978 by work on the trypsin-BPTI complex. Computers discriminated between good and bad models using a scoring function which rewarded large interface area, and pairs of molecules in contact but not occupying the same space. The computer used a simplified representation of the interacting proteins, with one interaction centre for each residue. Favorable electrostatic interactions, including hydrogen bonds, were identified by hand.
In the early 1990s, more structures of complexes were determined, and available computational power had increased substantially. With the emergence of bioinformatics, the focus moved towards developing generalized techniques which could be applied to an arbitrary set of complexes at acceptable computational cost. The new methods were envisaged to apply even in the absence of phylogenetic or experimental clues; any specific prior knowledge could still be introduced at the stage of choosing between the highest ranking output models, or be framed as input if the algorithm catered for it. 1992 saw the publication of the correlation method, an algorithm which used the fast Fourier transform to give a vastly improved scalability for evaluating coarse shape complementarity on rigid-body models. This was extended in 1997 to cover coarse electrostatics.
In 1996 the results of the first blind trial were published, in which six research groups attempted to predict the complexed structure of TEM-1 Beta-lactamase with Beta-lactamase inhibitor protein (BLIP). The exercise brought into focus the necessity of accommodating conformational change and the difficulty of discriminating between conformers. It also served as the prototype for the CAPRI assessment series, which debuted in 2001.
Read more about this topic: Macromolecular Docking
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