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A method for simultaneous alignment of multiple protein structures
Author(s) -
Shatsky Maxim,
Nussinov Ruth,
Wolfson Haim J.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10628
Subject(s) - multiple sequence alignment , structural alignment , pairwise comparison , computer science , sequence alignment , independence (probability theory) , sequence (biology) , protein structure , biological system , computational biology , algorithm , artificial intelligence , biology , peptide sequence , mathematics , genetics , biochemistry , statistics , gene
Here, we present MultiProt, a fully automated highly efficient technique to detect multiple structural alignments of protein structures. MultiProt finds the common geometrical cores between input molecules. To date, most methods for multiple alignment start from the pairwise alignment solutions. This may lead to a small overall alignment. In contrast, our method derives multiple alignments from simultaneous superpositions of input molecules. Further, our method does not require that all input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules in the input. To demonstrate the power of MultiProt, we provide a number of case studies. First, we demonstrate known multiple alignments of protein structures to illustrate the performance of MultiProt. Next, we present various biological applications. These include: (1) a partial alignment of hinge‐bent domains; (2) identification of functional groups of G‐proteins; (3) analysis of binding sites; and (4) protein‐protein interface alignment. Some applications preserve the sequence order of the residues in the alignment, whereas others are order‐independent. It is their residue sequence order‐independence that allows application of MultiProt to derive multiple alignments of binding sites and of protein‐protein interfaces, making MultiProt an extremely useful structural tool. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.