Analogy-based protein structure prediction: II. Testing of substitution matrices and pseudopotentials used to align protein sequences with spatial structures

The results of testing the recognition ability of various amino acid substitution matrices and manifold (both extracted from the literature and of our own design) pseudopotentials intended for the recognition of protein structures and sequence-to-structure alignments are described. The numerical estimates of the recognition ability of various substitution matrices and pseudopotentials were obtained for different levels of protein structure similarity. It is demonstrated that substitution matrices work much better than pseudopotentials at a high degree of sequence similarity of spatially similar proteins; however, some pseudopotentials outdo substitution matrices at a low level of sequence similarity between analogous proteins.