In this paper we present a method for flexible protein structure alignment based on elastic
shape analysis of backbones, in a manner that can incorporate different characteristics of …

We introduce an algorithm that uses the information gained from simultaneous consideration
of an entire group of related proteins to create multiple structure alignments (MSTAs) …

Abstract Background Hidden Markov Models (HMMs) have proven very useful in
computational biology for such applications as sequence pattern matching, gene-finding …

Motivation: Calculating multiple protein structure alignments (MSAs) is important for
understanding functional and evolutionary relationships between protein families, and for …

A general framework is presented for analyzing multiple protein structures. A family of
related protein structures may be analyzed using statistical regression methods. The …

MALECON is a progressive combinatorial procedure for multiple alignments of protein
structures. It searches a library of pairwise alignments for all three‐protein alignments in …

Surprisingly, after at least two decades of researches focused on the analysis of the
similarity between protein three-dimensional structures, several new comparison methods …

Background Remote homology detection is a challenging problem in Bioinformatics.
Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful …

The rapid increase in experimental data along with recent progress in computational
methods has brought modern biology a step closer toward solving one of the most …

Functional characterization of a protein sequence is one of the most frequent problems in
biology. In the absence of an experimentally determined structure, comparative or homology …