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M J Bayley

Publications and source records attributed to M J Bayley.

3 recordsLinked to original sources

Binning schemes for partition-based compound selection.

Partition-based approaches to the selection of structurally diverse sets of compounds involve allocating compounds to the individual elements of a multidimensional grid that spans the available chemical space. The space is defined by an appropriate set of chemical properties, with subranges of the values of these properties being used to define the constituent elements, or bins. This article compares several binning schemes in terms of their ability to provide an even distribution of compounds across the available space and to maximise the numbers of active molecules identified in simulated assay experiments.

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GENFOLD: a genetic algorithm for folding protein structures using NMR restraints.

We report the development and validation of the program GENFOLD, a genetic algorithm that calculates protein structures using restraints obtained from NMR, such as distances derived from nuclear Overhauser effects, and dihedral angles derived from coupling constants. The program has been tested on three proteins: the POU domain (a small three-helix DNA-binding protein), bovine pancreatic trypsin inhibitor (BPTI), and the starch-binding domain from Aspergillus niger glucoamylase I, a 108-residue beta-sheet protein. Structures were calculated for each protein using published NMR restraints. In addition, structures were calculated for BPTI using artificial restraints generated from a high-resolution crystal structure. In all cases the fittest calculated structures were close to the target structure, and could be refined to structures indistinguishable from the target structures by means of a low-temperature simulated annealing refinement. The effectiveness of the program is similar to that of distance geometry and simulated annealing methods, and it is capable of using a very wide range of restraints as input. It can thus be readily extended to the calculation of structures of large proteins, for which few NOE restraints may be available.

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