nucleotide interaction
catalytic activity
Zn ion binding
Fe ion binding
Cu ion binding
Cu ion binding
enolase superfamily template
haloacid dehalogenase superfamily template
double CH/π interaction motif
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Fit3D is a bioinformatics web service to search for spatial residue patterns in proteins, so-called structural motifs. Such motifs play key roles in clarification of linkage between protein structure and function, which is still a demanding process. Fortunately, the comparison of three-dimensional residue patterns can aid the functional comprehension. However, there is an urgent need for up-to-date and versatile computational resources to search for local similarities. Fit3D bridges the gap between easy usability and highly accurate pattern matching. Beside the online version there is also a versatile command line implementation available.

Features and advantages

Fit3D offers a variety of features and was shown to be an efficient and sensitive search method (Kaiser et al. 2015 ). Beside easy usage there are several advantages over existing approaches:

  • definition of position-specific exchangeDefinitions (PSEs) for structural motif search
  • detection of intra- and inter-molecular occurrences (especially relevant for interaction sites)
  • definition of arbitrary atoms used for motif alignment