In this paper, we present a perspective on the use of phylogenetic and structural analyses for improving the inference of protein function. Keywords: protein; function prediction; phylogeny; structure; structural classification; phylogenomicsKimmen Sjölander...
1.5.4Databases for structural classification of proteins Murzin et al. (1995)constructed theSCOPdatabase, which provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structures. For each protein, the classification has...
SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540 (1995). Article CAS PubMed Google Scholar Orengo, C. A. et al. CATH–a hierarchic classification of protein domain structures. Structure 5, 1093–1109 (...
Based on the type, amount and arrangement of the secondary structural elements, a protein can be classified into several structural classes. Structural Classification of Proteins (SCOP) [4] is a manually annotated database and has been regarded as the most accurate classification of protein structura...
Classification of protein groups with considerably lower (25–40%) homology remained more challenging18,28,29, while recent investigations seem to have successfully overcome the 80% accuracy barrier even for the low homology datasets30,31. A number of mathematical approaches has been utilized, ...
In a second test, we quantify the ability of the significance score of the alignments to recognize structural and evolutionary relationships. As a benchmark we use a representative set of the SCOP (structural classification of proteins) database, with similarities ranging from closely related ...
structural classification of proteins PDB: protein data bank RMSD: root mean square deviation Rvs: ratio of volume over area.References Kendrew JC, Dickerson RE, Strandberg BE, Hart RG, Davies DR, Phillips DC, Shore VC: Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A...
PROTEIN FOLD RECOGNITION BASED ON STRUCTURAL CLASSIFICATION基于结构分类的蛋白质折叠模式识别方法蛋白质折叠模式识别结构分类平均势SCOPThreading对用于折叠模式识别的蛋白质结构数据库进行结构分类,构建了四个分类库:Al-α库,Al-β库,α/β库,α+β库和一个总库,然后分别统计出不同灵敏度的匹配评估函数(平均势)....
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM: CATH-a hierarchic classification of protein domain structures. Structure. 1997, 5 (8): 1093-1108. 10.1016/S0969-2126(97)00260-8. Article CAS PubMed Google Scholar Sonnhammer EL, Eddy SR, Durbin R: Pfam: a comprehe...
A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering ...