Predicting substrate specificity of adenylation domains of nonribosomal peptide synthetases and other protein properties by latent semantic indexing

• Published in: Journal of industrial microbiology & biotechnology Vol. 41; no. 2; pp. 461 - 467
• Main Authors: Baranašić, Damir, Zucko, Jurica, Diminic, Janko, Gacesa, Ranko, Long, Paul F, Cullum, John, Hranueli, Daslav, Starcevic, Antonio
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.02.2014; Oxford University Press; Springer Berlin Heidelberg
• Subjects: amino acid sequences; Amino Acids; Amino Acids - chemistry; Analysis; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Biosynthesis; Biotechnology; Catalytic Domain; chemistry; classification; Decomposition; Documents; Genetic Engineering; Genomes; Genomics; Inorganic Chemistry; Kinases; Life Sciences; ligases; Linear algebra; metabolism; Metabolites; methods; Microbiology; Original Article; Peptide Synthases; Peptide Synthases - chemistry; Peptide Synthases - classification; Peptide Synthases - metabolism; Peptides; prediction; Proteins; Semantics; Sequence Alignment; Sequence Analysis, Protein; Sequence Analysis, Protein - methods; Studies; Substrate Specificity; Substrates; Adenylation domains; Functional subtype; LSI; NRPS; Protein tokenization

Successful genome mining is dependent on accurate prediction of protein function from sequence. This often involves dividing protein families into functional subtypes (e.g., with different substrates). In many cases, there are only a small number of known functional subtypes, but in the case of the...