An improved profile-level domain linker propensity index for protein domain boundary prediction. Protein Pept Lett 2011 Jan;18(1):7-16
Date
10/20/2010Pubmed ID
20955175DOI
10.2174/092986611794328717Scopus ID
2-s2.0-78751536327 (requires institutional sign-in at Scopus site) 15 CitationsAbstract
Protein domain boundary prediction is critical for understanding protein structure and function. In this study, we present a novel method, an order profile domain linker propensity index (OPI), which uses the evolutionary information extracted from the protein sequence frequency profiles calculated from the multiple sequence alignments. A protein sequence is first converted into smooth and normalized numeric order profiles by OPI, from which the domain linkers can be predicted. By discriminating the different frequencies of the amino acids in the protein sequence frequency profiles, OPI clearly shows better performance than our previous method, a binary profile domain linker propensity index (PDLI). We tested our new method on two different datasets, SCOP-1 dataset and SCOP-2 dataset, and we were able to achieve a precision of 0.82 and 0.91 respectively. OPI also outperforms other residue-level, profile-level indexes as well as other state-of-the-art methods.
Author List
Zhang Y, Liu B, Dong Q, Jin VXAuthor
Victor X. Jin PhD Professor in the Institute for Health and Equity department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Amino Acid SequenceMolecular Sequence Data
Propensity Score
Protein Structure, Tertiary
Proteins
