Russell R B, Barton G J
Laboratory of Molecular Biophysics, University of Oxford, England.
Proteins. 1992 Oct;14(2):309-23. doi: 10.1002/prot.340140216.
An algorithm is presented for the accurate and rapid generation of multiple protein sequence alignments from tertiary structure comparisons. A preliminary multiple sequence alignment is performed using sequence information, which then determines an initial superposition of the structures. A structure comparison algorithm is applied to all pairs of proteins in the superimposed set and a similarity tree calculated. Multiple sequence alignments are then generated by following the tree from the branches to the root. At each branchpoint of the tree, a structure-based sequence alignment and coordinate transformations are output, with the multiple alignment of all structures output at the root. The algorithm encoded in STAMP (STructural Alignment of Multiple Proteins) is shown to give alignments in good agreement with published structural accounts within the dehydrogenase fold domains, globins, and serine proteinases. In order to reduce the need for visual verification, two similarity indices are introduced to determine the quality of each generated structural alignment. Sc quantifies the global structural similarity between pairs or groups of proteins, whereas Pij' provides a normalized measure of the confidence in the alignment of each residue. STAMP alignments have the quality of each alignment characterized by Sc and Pij' values and thus provide a reproducible resource for studies of residue conservation within structural motifs.
本文提出了一种算法，用于从三级结构比较中准确快速地生成多个蛋白质序列比对。首先利用序列信息进行初步的多序列比对，进而确定结构的初始叠加。将结构比较算法应用于叠加集中的所有蛋白质对，并计算相似性树。然后通过从树枝到树根追踪该树来生成多序列比对。在树的每个分支点，输出基于结构的序列比对和坐标变换，在树根处输出所有结构的多序列比对。结果表明，编码在STAMP（多蛋白结构比对）中的算法所给出的比对结果与已发表的关于脱氢酶折叠域、球蛋白和丝氨酸蛋白酶结构描述高度一致。为了减少视觉验证的需求，引入了两个相似性指标来确定每个生成的结构比对的质量。Sc量化了蛋白质对或蛋白质组之间的全局结构相似性，而Pij'提供了每个残基比对置信度的归一化度量。STAMP比对中每个比对的质量由Sc和Pij'值表征，从而为研究结构基序内的残基保守性提供了一个可重复的资源。
