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Figure 4 | BMC Bioinformatics

Figure 4

From: Prediction of indirect interactions in proteins

Figure 4

Outline of the mapping of direct and indirect interactions in molecular recognition using proteochemometrics. Outline of a general procedure for mapping molecular recognition by biomacromolecules. Initially, sets of wild-type macromolecules are identified. Using statistical molecular design a library is then created from the wild-type macromolecules. The library can be selected from the wild-type molecules if the initial collection contains sufficient chemical variation. Chemical variation may also be introduced artificially by mutagensis. Shuffling sequence fragments can then be used to create a library, where three or more segments and three or more macromolecules are used as the starting point. After evaluating the interaction of the library with a suitable library of ligands of interest, a proteochemometric model can be created. This model may be used to localize the regions in each macromolecule that contribute to the selectivity of each particular ligand evaluated. It may happen that it is not possible to unambiguously localize individual amino acids within a particular region, due to co-varying amino acid positions in the macromolecular library. In that case, an extension of the library can be made in order to resolve the ambiguity.

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