Gaussian-based alignment of protein structures: Deriving a consensus superposition when alternative solutions exist
The use of a Gaussian-based representation of protein structures for evaluating protein-structure similarities and deriving three-dimensional superpositions is presented. The approach, as implemented in the program GAPS, is applied to three pairs of proteins with different topological characteristics (rich alpha-helix, mixed alpha-helix/beta-strand, and rich beta-strand), low sequence identities (10-30%), and recognized difficulties to define a unique optimum alignment. Validation of the GAPS superpositions is done by comparison with superpositions obtained by the TOP, GA_FIT, and ALIGN programs and those directly extracted from the FSSP database. Results suggest that a Gaussian-based methodology offers an objective means to, depending on the Gaussian-based representation, derive a consensus three-dimensional superposition when alternative superposition solutions exist.
protein similarity protein structure comparison protein structure superposition consensus alignment