Ochagavía María Elena, Wodak Shoshana
Center for Genetic Engineering and Biotechnology, Cubanacán, La Habana, Cuba.
Proteins. 2004 May 1;55(2):436-54. doi: 10.1002/prot.10587.
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 which a specified number of residues is consistently aligned. These alignments are progressively expanded to include additional proteins and more spatially equivalent residues, subject to certain criteria. This action involves superimposing the aligned proteins by their hitherto equivalent residues and searching for additional Calpha atoms that lie close in space. The performance of MALECON is illustrated and compared with several extant multiple structure alignment methods by using as test the globin homologous superfamily, the OB and the Jellyrolls folds. MALECON gives better definitions of the common structural features in the structurally more diverse proteins of the OB and Jellyrolls folds, but it yields comparable results for the more similar globins. When no consistent multiple alignments can be derived for all members of a protein group, our procedure is still capable of automatically generating consistent alignments and common core definitions for subgroups of the members. This finding is illustrated for proteins of the OB fold and SH3 domains, believed to share common structural features, and should be very instrumental in homology modeling and investigations of protein evolution.
MALECON是一种用于蛋白质结构多重比对的渐进组合程序。它在成对比对库中搜索所有三蛋白质比对，其中指定数量的残基始终对齐。这些比对会逐步扩展，以纳入更多蛋白质和更多空间等效残基，但需符合某些标准。此操作包括通过迄今等效的残基对已比对的蛋白质进行叠加，并搜索在空间上靠近的额外α碳原子。通过使用球蛋白同源超家族、OB和果冻卷折叠作为测试，展示了MALECON的性能并与几种现有的多重结构比对方法进行了比较。对于OB和果冻卷折叠中结构更多样化的蛋白质，MALECON能更好地定义其共同结构特征，但对于更相似的球蛋白，它产生的结果相当。当无法为蛋白质组的所有成员得出一致的多重比对时，我们的程序仍能够自动为成员的子组生成一致的比对和共同核心定义。这一发现针对被认为具有共同结构特征的OB折叠和SH3结构域的蛋白质进行了说明，并且在同源建模和蛋白质进化研究中应该非常有用。
