TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)
Given the amino acid sequence of a putative alpha-helical membrane protein, SCAMPI predicts the topology of the protein, i.e. a specification of the membrane spanning segments and their IN/OUT orientation relative to the membrane.
TopoGSA (Topology-based Gene Set Analysis) computes and visualise the topological properties of a set of genes/proteins mapped onto a molecular interaction network. Different topological characteristics, such as the centrality of nodes in the network or their tendency to form clusters, are computed and compared against those of known cellular pathways and processes (KEGG, BioCarta, GO, etc.).
TORQUE is a tool for cross-species querying of protein-protein interaction networks. Given a complex (set of proteins) for a query species, Torque seeks a matching set of proteins of a target species that are sequence-similar to the query proteins and span a connected region of the target network.
HMMpTM is a Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.