Pandit Shashi Bhushan, Skolnick Jeffrey
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA.
BMC Bioinformatics. 2008 Dec 12;9:531. doi: 10.1186/1471-2105-9-531.
Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true.
To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TM-align, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (9%) and coverage (7%) in comparison to those generated by TM-align. Fr-TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align.
Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr-TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.
蛋白质三级结构比较应用于当代结构生物学的各个领域。大多数结构比较方法都涉及生成初始种子比对，然后对其进行扩展和/或优化，以根据结构比较指标评估在一对蛋白质结构之间提供最佳的结构叠加。其中一种指标，即TM分数，最近被引入，以提供一对结构之间坐标均方根偏差和覆盖率的综合结构质量度量。利用TM分数，开发了TM-align结构比对算法，该算法通常被发现比最常用的结构比对程序具有更高的准确性和覆盖率；然而，在许多情况下并非如此。
为了进一步提高结构比对质量，开发了Fr-TM-align算法，其中使用比对的片段对来生成初始种子比对，然后使用动态规划进行优化，以最大化TM分数。为了评估Fr-TM-align与其他程序（如CE和TM-align）相比的结构比对质量，我们检查了各种比对质量评估分数，如PSI和TM分数。评估表明，与CE和TM-align相比，Fr-TM-align的结构比对质量更好。平均而言，与TM-align生成的结构比对相比，使用Fr-TM-align生成的结构比对具有更高的TM分数（约9%）和覆盖率（约7%）。Fr-TM-align使用穷举程序来生成初始种子比对。因此，该算法在计算上比TM-align更昂贵。
Fr-TM-align是一种采用片段比对和组装的新算法，与TM-align相比，它能提供更好的结构比对。Fr-TM-align的源代码和可执行文件可从以下网址免费下载：http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/ 。
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