Allows scientists to store, share and publicly distribute biological networks as dynamic actionable data, and develop applications using them. NDEx is an online “commons”, a scientist driven data exchange, permitting users to search and browse networks, establish accounts, create or join groups, and upload, export, download, and administer networks. The platform aims to enable experimentation with novel forms of scientific review and discourse.
A database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo sapiens. Nearly all existing algorithms for orthology detection are based on sequence comparison. The IsoBase database may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword.
A method based on comparing similarity of protein surfaces. PEVOSOAR predicts protein functions by solving the problem of uncovering residue substitution pattern due to protein function and separating it from substitution pattern due to protein folding. This method also computes a profile which characterizes protein binding activities that may involve multiple substrates or ligands. PEVOSOAR correctly identified 131 structures as alpha amylase.
A comprehensive database of synthetic lethality (SL). SL pairs were collected from multiple sources, including biochemical assays, other related databases, computational predictions and text-mining outputs for five species. Furthermore, a user-friendly web interface has been implemented to facilitate data analysis and interpretation. With the integrated data sets and analytics functionalities, SynLethDB would be a useful resource for biomedical research community and pharmaceutical industry.
Gathers diagrams depicting dealing with processes linked with Arabidopsis embryo and seed development. RIMAS is a repository reporting regulatory pathways and genetic interactions between transcription factors, hormonal pathways, or epigenetic processes. All the maps are standardized according to the systems biology graphical notation (SBGN) nomenclature, linked to their corresponding scientific literature and can be downloaded in common exchange formats.
Summarizes hydrogen bonding in a dataset of high-resolution protein structures. Atlas of Side-Chain and Main-Chain Hydrogen Bonding is a repository that provides the distribution of the frequencies and geometries of hydrogen bonds formed by main-chain and side-chain donors and acceptors. The database can be useful for users who would like to know whether the hydrogen bonding in their model is normative.
Provides information about diverse data on protein folding kinetics. KineticDB is a relational database that contains single-domain proteins, and separates protein domains and short peptides without disulfide bonds in their native structure. Each record of the database relates to a single protein folding kinetics measurement extracted from the original paper and gives details of the experimentally studied protein, its best available tertiary structure, experimental conditions, reference to the original paper and experimental results.