Structural motifs are important for the integrity of a protein fold and can be employed to design and rationalize protein engineering and folding experiments. Such conserved segments represent the conserved core of a family or superfamily and can be crucial for the recognition of potential new members in sequence and structure databases.
A browser-database for protein structure/function. OCA database integrates information from KEGG, OMIM,PDBselect, Pfam, PubMed, SCOP, SwissProt, and others. It provides rich content annotation on structure and function, generating dynamic links to these external sources. This database offers simple search, FASTA search or many options for additional searches. It also allows the user to save the generated search results.
Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant genomes as physical references in order to gather and merge available genomic data from in silico or experimental approaches. Combining original data with the output of experts and graphical displays that differ from classical plant genome browsers, FLAGdb presents a powerful complementary tool for exploring plant genomes and exploiting structural and functional resources, without the need for computer programming knowledge.
A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
A series of databanks that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per PDB entry. Several of the well-established databanks such as HSSP, PDBREPORT and PDB_REDO have been updated and/or improved.
A database that contains recalculated structures for 500+ protein entries from the Protein Data Bank (PDB). RECOORD can be used by the structural biology community for further development of calculation protocols, validation tools, structure-based statistical approaches and modeling.
A detailed, searchable repository of coiled-coil assignment. Coiled coils were identified using the program SOCKET, which locates coiled coils based on knobs-into-holes packing of side chains between alpha-helices.