Meta-DP: domain prediction meta-server
Bioinformatics
Analyzing functional similarity of protein sequences with discrete wavelet transform
Computational Biology and Chemistry
Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase
Computational Biology and Chemistry
Investigating protein domain combinations in complete proteomes
Computational Biology and Chemistry
Research Article: Exploiting three kinds of interface propensities to identify protein binding sites
Computational Biology and Chemistry
Prediction of protein protein interactions from primary sequences
International Journal of Data Mining and Bioinformatics
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Successful prediction of protein domain boundaries provides valuable information not only for the computational structure prediction of multi-domain proteins but also for the experimental structure determination. In this work, a novel index at the profile level is presented, namely, the profile domain linker propensity index (PDLI), which uses the evolutionary information of profiles for domain linker prediction. The frequency profiles are directly calculated from the multiple sequence alignments outputted by PSI-BLAST and converted into binary profiles with a probability threshold. PDLI is then obtained by the frequencies of binary profiles in domain linkers as compared to those in domains. A smooth and normalized numeric profile is generated for any amino acid sequences from which the domain linkers can be predicted. Testing on the Structural Classification of Proteins (SCOP) database and CASP6 targets shows that PDLI outperforms other indexes at the amino acid level.