SimRNAweb offers a web interface to support most of the features of the program SimRNA and offers some unique setup features of its own that can be used by advanced users. There is no need to download programs, run programs with various command line options or find the support and resources (80 cores, computational disk space, etc.) of a high performance computing facility.
The program SimRNA can carry out de novo folding of RNA sequences using only the sequence information or can accept a PDB file containing an RNA structure in any state of folding (obtained either from experiment or from a simulation). When starting with a PDB file with a RNA structure in some folding trajectory, the user can either carry out coarse-grained refinements or search the general trajectory of folding from such a starting structure. In benchmark tests, SimRNA was able to recapitulate the secondary structure and 3D structure with fairly high accuracy, including correct prediction of pseudoknots. SimRNA can also fold an RNA sequence under a variety of restraints including secondary structure restraints, distance restraints and, when a PDB file is supplied, parts of the structure in the PDB file can be frozen while other parts are allowed to be flexible.
All of these features and more are provided with the SimRNAweb server and, in many cases, this does not require the reformating of PDB files. SimRNAweb accepts any form or combination of restraints including secondary structure dot bracket notation, distance restraints, and, when one has a PDB file, the position of specific residues can be frozen (while leaving other residues free) by simply indicating the RNA chain and residue index. In addtion, a unique function on the server is the ability to add missing residues to a PDB structure. This allows the possibility of building a complete structure from a PDB file of a crystal structure determination where there are numerous gaps in the sequence.
Since restraints can be derived from experimental or computational analyses (including information about secondary structure and/or long-range contacts) it is possible to use this information in de novo folding or refinement of RNA molecules. With some advanced effort, molecules with folds, pockets, exposed or buried regions of structure can be explored. Moreover, since the trajectory files can also be obtained, SimRNAweb can be used to analyze conformational landscapes and identify potential alternative structures.