Bhaduri A, Pugalenthi G, Gupta N, Sowdhamini R
National Centre for Biological Sciences, Tata Institute of Fundamental Research, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, Karnataka, India.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W602-5. doi: 10.1093/nar/gkh375.
Functional selection and three-dimensional structural constraints of proteins relate to the retention of significant sequence similarity between proteins of similar fold and function despite poor overall sequence identity and evolutionary pressures. We report the availability of 'iMOT' (interacting MOTif) server, an interactive package for the automatic identification of spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage. Spatial interactions between conserved stretches of a protein are evaluated by calculations of pseudo-potentials that describe the strength of interactions. Such an evaluation permits the automatic identification of highly interacting conserved regions of a protein. Interacting motifs have been shown to be useful in searching for distant homologues and establishing remote homologies among the largely unassigned sequences in genome databases. Information on such motifs should also be of value in protein folding, modelling and engineering experiments. The iMOT server can be accessed from http://www.ncbs.res.in/~faculty/mini/imot/iMOTserver.html. Supplementary Material can be accessed from: http://www.ncbs.res.in/~faculty/mini/imot/supplementary.html.
蛋白质的功能选择和三维结构限制与具有相似折叠和功能的蛋白质之间显著序列相似性的保留有关，尽管总体序列同一性较差且存在进化压力。我们报告了“iMOT”（相互作用基序）服务器的可用性，这是一个交互式软件包，用于自动识别具有相似折叠且拥有共同祖先谱系的远缘相关蛋白质之间的空间相互作用基序。通过计算描述相互作用强度的伪势来评估蛋白质保守片段之间的空间相互作用。这种评估允许自动识别蛋白质的高度相互作用保守区域。已证明相互作用基序在搜索远缘同源物以及在基因组数据库中大部分未分类序列之间建立远程同源性方面很有用。关于此类基序的信息在蛋白质折叠、建模和工程实验中也应具有价值。可从http://www.ncbs.res.in/~faculty/mini/imot/iMOTserver.html访问iMOT服务器。补充材料可从：http://www.ncbs.res.in/~faculty/mini/imot/supplementary.html访问。
