Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity.
BACKGROUND
Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midnight-" zones where pair-wise sequence identities to known sequences fall below 25% and sequence-based functional annotations often fail.


RESULTS
Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in "immunoevasins", proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method.


CONCLUSIONS
We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty.
Jia
Yi
Y
Department of Electrical Engineering & Computer Science, University of Kansas, Lawrence, KS, 66045, USA. jiayi@ittc.ku.edu
Huan
Jun
J
Buhr
Vincent
V
Zhang
Jintao
J
Carayannopoulos
Leonidas N
LN
D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
D011506:Proteins