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We propose new empirical scoring potentials and associated alignment procedures for optimally aligning protein sequences to protein structures. The method has two main applications: first, the recognition of a plausible fold for a protein sequence of unknown structure out of a database of representative protein structures and, second, the improvement of(More)
Fast growth of the number of the solved protein structures is increasing the role of their comparative analysis. In this paper I describe a new program, SARF2, for protein structure comparison and discuss new examples of the non-topological structural resemblance. SARF2 is designed to detect ensembles of secondary structure elements, which form similar(More)
A new algorithm for aligning several sequences based on the calculation of a consensus matrix and the comparison of all the sequences using this consensus matrix is described. This consensus matrix contains the preference scores of each nucleotide/amino acid and gaps in every position of the alignment. Two modifications of the algorithm corresponding to the(More)
The paper describes a new software package DNASUN developed for supporting gene engineering laboratories. The package provides a user-friendly interface for experimental researches and supports the traditional nucleotide/protein sequence analysis as well as physical mapping, sequencing, plasmid manipulations, optimal oligonucleotide probe selection and(More)
We have developed a new method and program, SARF2, for fast comparison of protein structures, which can detect topological as well as nontopological similarities. The method searches for large ensembles of secondary structure elements, which are mutually compatible in two proteins. These ensembles consist of small fragments of C alpha-trace, similarly(More)
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