PALSSE (Predictive Assignment of Linear Secondary Structure Elements) is a software that delineates secondary structure elements (SSEs) from protein Cα coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and β-strand, typically those that can be well approximated by vectors. In contrast to traditional secondary structure algorithms, which identify a secondary structure state for every residue in a protein chain, our program attributes residues to linear SSEs. Consecutive elements may overlap, thus allowing residues located at the overlapping region to have more than one secondary structure type.
MASS is an efficient method for multiple alignment of protein structures and detection of structural motifs. Exploiting the secondary structure representation aids in filtering out noisy results and in making the method highly efficient and robust. MASS disregards the sequence order of the secondary structure elements. Thus, it can find non-sequential and even non-topological structural motifs. An important novel feature of MASS is subset alignment detection: It does not require that all the input molecules be aligned. Rather, MASS is capable of detecting structural motifs shared only by a subset of the molecules.
RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.
MEMERIS (Muptiple Em for Motif Elucidation in Rna’s Including Secondary Structures) integrates information about RNA secondary structures into the motif search to guide the search towards single-stranded regions.
RNA-DV (RNA Design & Visualization) is a flexible and powerful tool targeted at visualization and modification of RNA secondary structure. Compare to existing software applications, RNA-DV set itself apart by not only providing an editing and visualization interface but also integrates thermodynamic energies for the current structure design. RNA-DV aims at providing an easy-to-use GUI for visualizing and designing RNA secondary structures. It allows users to interact directly with the RNA structure and perform operations such as changing primary sequence content and connect/disconnect nucleotide bonds. It also integrates thermodynamic energy calculations including four major energy models. RNA-DV recognizes three input formats including CT, RNAML and dot bracket (dp).