[Protein structure prediction from analogy. II. Testing of substitution matrices and pseudo-potentials used to align protein sequences with folds].

: The paper describes results of testing of "recognition ability" of different substitution matrices and various pseudo-potentials (taken from literature or designed by us) to recognize protein structures and produce the sequence-to-structure alignments. Numerical estimates of "identifying power" of various matrices and pseudo-potentials are obtained for different levels of similarity between amino acid sequences of spatially-similar proteins. It is shown that substitution matrices work much better than pseudo-potentials at a high level of similarity of sequences of spatially-similar proteins, but some pseudo-potentials overcome substitution matrices at a low level of sequence similarity.