Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach—combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species. iPTMnet encompasses data from (i) our PTM-focused text mining tools, RLIMS-P and eFIP, which extract phosphorylation information from full-scale mining of PubMed abstracts and full-length articles; (ii) a set of curated databases with experimentally observed PTMs; and iii) Protein Ontology that organizes proteins and PTM proteoforms, enabling their representation, annotation and comparison within and across species. Presently covering eight major PTM types (phosphorylation, ubiquitination, acetylation, methylation, glycosylation, S-nitrosylation, sumoylation and myristoylation), iPTMnet knowledgebase contains more than 654 500 unique PTM sites in over 62 100 proteins, along with more than 1200 PTM enzymes and over 24 300 PTM enzyme-substrate-site relations. The website supports online search, browsing, retrieval and visual analysis for scientific queries. Several examples, including functional interpretation of phosphoproteomic data, demonstrate iPTMnet as a gateway for visual exploration and systematic analysis of PTM networks and conservation, thereby enabling PTM discovery and hypothesis generation.

Three new flavonoids, (3R)-4'-methoxy-2',3,7-trihydroxyisoflavanone (11), 7-methoxy-3,3',4',6-tetrahydroxyflavone (18), and 2',7-dihydroxy-4',5'-dimethoxyisoflavone (22), were isolated from the heartwood of Dalbergia odorifera T. Chen. (Leguminosae), together with twenty-two known compounds, (S)-4-methoxydalbergione (1), cearoin (2), medicarpin (3), formononetin (4), sativanone (5), 3-hydroxy-9-methoxy-coumestan (6), meliotocarpan A (7), isoliquiritigenin (8), stevein (9), liquiritigenin (10), 3',4',7-trihydroxyflavanone (12), butein (13), 3'-hydroxymelanettin (14), koparin (15), bowdichione (16), fisetin (17), melanettin (19), sulfuretin (20), 3'-hydroxydaidzein (21), 3'-O-methylviolanone (23), xenognosin B (24), and dalbergin (25). These flavonoids were evaluated in antiallergic and anti-inflammatory tests. The results showed that (S)-4-methoxydalbergione (1) and cearoin (2) exhibited antiallergic activity while (S)-4-methoxydalbergione (1), cearoin (2), butein (13), koparin (15), bowdichione (16), 3'-O-methylviolanone (23), and xenognosin B (24) showed significant anti-inflammatory activity.

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.

Panaxynol and ginsenosides Ro, Rg1, and Rg2 were found to be the main antiplatelet components in the diethyl ether and 1-butanol fractions, respectively, during the activity-guided fractionation of Panax ginseng, Panaxynol inhibited the aggregation, release reaction, and thromboxane formation in rabbit platelets while ginsenosides Ro, Rg1, and Rg2 suppressed the release reaction only.

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Eight new prenylated flavonoids, ugonins M-T (1-8), together with five known compounds, ugonins J-L (9-11), 5,4'-dihydroxy-4'',4''-dimethyl-5''-methyl-5''H-dihydrofurano[2'',3'':6,7]flavanone, and quercetin, were isolated and purified from the rhizomes of Helminthostachys zeylanica. The structures of the new isolates were elucidated by spectroscopic and chemical methods. Compounds 1, 3, 5, 7, 8, and 11 showed inhibition of superoxide anion generation and elastase release by human neutrophils in response to formyl-l-methionyl-l-leucyl-l-phenylalanine/cytochalasin B (FMLP/CB).

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