TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

BMC Bioinformatics

Table 4 Flexible and rigid FATCAT and TOPS++FATCAT comparison results for d2trxa_ and d1kte_

Methods	Optimal RMSD (Å)	Chain RMSD (Å)	Optimal length	Alignment length/gaps	Score	P-value	Sequence Identity (%)	Sequence Similarity (%)	AFPs
Flexible_FATCAT	3.48	5.14	86	107/21	125.51	3.29e-03	9.35	25.23	3,092
rigid_FATCAT	3.06	3.14	88	109/21	123.09	7.14e-5	10.09	25.69	3,092
flexible_TOPS++FATCAT	3.06	1.67	88	109/21	110.05	2.08e-04	10.09	25.69	323
rigid_TOPS++FATCAT	3.06	1.67	88	109/21	110.05	2.08e-04	10.09	25.69	323

Optimal RMSD: The root mean square deviation (RMSD) of aligned Cα atoms of the input structures, with one input structure rearranged if flexibility is detected (i.e., twists are introduced in the alignment). Chain RMSD: The RMSD of aligned Cα atoms of the input structures, without structural rearrangement even if structural flexibility is detected in the alignment. Optimal Length: The number of equivalent positions of the alignment; P-value. P-value is the probability of observing a greater score used in FATCAT to evaluate the significance of structural similarity detected by FATCAT. AFPs: Aligned Fragment Pairs. For further information, please refer to the FATCAT help page available at the following web site: http://fatcat.burnham.org/fatcat/fatcathelp.html

ISSN: 1471-2105