SimRNA is available for academic users under the (details enclosed in the license file to be found in each package). no modified residues are supported as of yet). In the current version readable residues are A, C, G and U only (i.e. The PDB format should be simply the structure of the RNA with no heteroatoms or unusual names. SimRNA can be initiated with input files that include either the RNA sequence (or sequences) in a single line (similar to the Vienna format) or in the form of a structure written in PDB format. SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction. SimRNA - a tool for simulations of RNA conformational dynamics, including RNA 3D structure prediction *The classification is expected to evolve as new data become available and we would like to encourage all interested parties to submit their suggestions for improvement as well as 3D structure predictions* Compared to other databases, RNArchitecture is unique in its focus on structure-based RNA classification, and in providing a platform for storing RNA 3D structure predictions. RNArchitecture also presents theoretical models of RNA 3D structure and is open for submission of structural models by users. For each Family with an experimentally determined 3D structure(s), a representative one is provided. Some groups at different levels of the hierarchy are currently labeled as “unclassified”. The highest level, Class, organizes Families into very broad structural categories, such as simple or complex structured RNAs. Similar structures are further grouped into Architectures. Evolutionarily related Families are grouped into Superfamilies. Consensus structures of Families are described with a reduced secondary structure representation. Its central level is Family, which builds on the Rfam catalog, and gathers closely related RNAs. The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities.
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