TCMPG: TCM Plant Genome Database

Although hundreds of medical plants have been sequenced, the related data were scattered at different sources, which hindered the systematical researches on medical plants. To solve such a challenge, we proposed the integrative database for Traditional Chinese Medicine Plant Genome (TCMPG). TCMPG not only deposits the genome data of traditional Chinese medical plants, but also provides a series of computational tools for researchers to perform systematical analysis. At present, 160 kinds of plants, 195 corresponding genomes, and 255 herbs (different parts from the same plant), together with the related information on plant species, genomes, and herbal medicines were included in TCMPG.

INPUT: An Intelligent Network Pharmacology Platform Unique for Traditional Chinese Medicine

With more than 2,000 years of knowledge accumulation and clinical practice, Traditional Chinese Medicine (TCM) has become an important part of modern medicine. The characteristics of TCM are multiple components, multiple targets, and multiple pathways, which coincide with the multiple factors and complex pathological characteristics of diseases. However, these characteristics also exerted challenges to decoding the disease treatment mechanisms of TCM.

KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides

KNIndex is the abbreviation of K-Nucleotides Index database. The database deposits the original and standardized values of the physicochemical properties for k-tuple nucleotides (k = 1, 2, 3).

RNAWRE: a resource of writers, readers and erasers of RNA modifications

RNA modifications provided a new layer of post-transcriptional gene regulation. Increasing evidences have demonstrated that the function of RNA modifications is determined by RNA-modifying proteins that contains three classes of proteins: writers, readers and erasers. Writers are proteins that place specific modifications on RNA. Readers are proteins that bind selectively to modified forms of RNA. Erasers are proteins that remove the specific modifications on RNA. The current version of RNAWRE collected more than 2045 manually curated writers, readers and erasers for the 6 major kinds of RNA modifications, namely Cap, m1A, m6A, m5C, ψ and Poly A. These proteins are from animals. RNAWRE will be helpful in revealing the mechanisms of RNA modifications.

Pro54DB: a database for experimentally verified sigma-54 promoters

Pro54DB is a primary database on σ54 promoters and transcriptional regulation information curated from original scientific publications.

AOD: a database for the antioxidant protein

Antioxidant proteins are a kind of molecules that can interact with and neutralize free radicals. By donating an electron to rampaging free radicals, antioxidant proteins can terminate the chain reactions caused by free radical intermediates. This protects the cells from further damage or death. The use of antioxidant proteins in pharmacology is intensively studied in recent years. Antioxidant proteins have been investigated for the prevention of diseases such as cancer, coronary heart disease, and even altitude sickness.
AOD (the antioxidant protein database) is a manually curated database of experimentally validated antioxidant proteins. Information including taxonomy, source organism, subcellular location, gene ontology, catalytic activity and function of antioxidant proteins are all extracted from UniProtKB/Swiss-Prot (release 2016_11) and captured in AOD. In addition, links to external databases like SwissProt, NCBI,and Gene Ontology are also provided. As a user-friendly database, a support vector machine based antioxidant protein prediction model, namely AodPred and the sequence analysis tool BLAST are also integrated in the AOD.