很少有研究是完全新颖的,TM-score 也不例外,它其实是LG-score的改进MaxSub的改进。 1997年,Michael Levitt,这位日后的诺贝尔奖得主,与他的博后Mark Gerstein,目前耶鲁大学生物医学信息学、分子生物物理与生物化学、计算机学的三聘教授,出于统一比较蛋白序列相似度和结构相似度的想法,提出了Levitt-Gerstein score,也就是...
TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005;33(7):2302-2309. 2. Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics. 2010;26(7):889-895. 3. Yang Y, ZhouY. Specific interactions ...
With a TM-score at 0.5, for instance, its P-value is 5.5 x 10(-7), which means we need to consider at least 1.8 million random protein pairs to acquire a TM-score of no less than 0.5. Second, we examine the posterior probability of the same fold proteins from three datasets SCOP,...
This finding indicates that TM-score can be used as an approximate but quantitative criterion for protein topology classification, i.e. protein pairs with a TM-score >0.5 are mostly in the same fold while those with a TM-score <0.5 are mainly not in the same fold. Contact: zhng@...
4.1)采用蛋白质结构比对工具TM-align,依次计算每个单域蛋白和模板蛋白之间的比对得分,记录为TM-score<Sub>1</Sub>,TM-score<Sub>2</Sub>,...,TM-score<Sub>n</Sub>,其中TM-score<Sub>n</Sub>是第n个单域蛋白和模板蛋白之间的比对得分,n为单域蛋白的总个数; 4.2)以步骤3.1)中单域蛋白比对最高的得分...
We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is approximately 4 times faster than CE and 20 times faster than DALI and SAL. On average, the res...
4.1)采用蛋白质结构比对工具tm-align,依次计算每个单域蛋白和模板蛋白之间的比对得分,记录为tm-score1,tm-score2,…,tm-scoren,其中tm-scoren是第n个单域蛋白和模板蛋白之间的比对得分,n为单域蛋白的总个数; 4.2)以步骤3.1)中单域蛋白比对最高的得分为该模板的局部评价得分lscore,即lscore=max(tm-score1,tm...
Python implementation of the TMscore program to compare structures of the same protein. Usage: We provide three classes, TMscoring, Sscoring, and RMSDscoring, that only differ in their default optimisation score. They are initialised with the file paths to two PDB files: alignment = tmscoring....
Tab.4 The correlation analysis of TM,TAT,PIC and t-PAIC with SOFA and APACHEⅡ score in septic DIC group 3讨 论 DIC不是一种独立的疾病,多种疾病均可伴随凝血功能障碍,疾病进展可导致休克、多器官功能衰竭,严重感染特别...
protein chains from the Protein Data Bank (PDB) with a sequence identity cutoff <95%: 1996 distinct folds are found when a TM-score threshold of 0.5 is used. We also use TM-align to match the models predicted by TASSER for solved non-homologous proteins in PDB. For both folded and ...