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
© 2018 bioinformatics group Mittweida | Fit3D received 42 jobs in total | current job load: 0 jobs
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Toolbox

Å
How to use the Toolbox?
Structure viewer

The Fit3D webserver implements the JavaScript-based Protein Viewer from Marco Biasini . The zoom level can be controlled with the mouse wheel. You can manipulate the point of view by pressing the middle mouse button or by holding down the Shift-key. To center the point of view double click with the left mouse button.

One against one alignment for a single match found by Fit3D. The green ball-stick structure represents the query motif. Residues of the query motif are labeled in green, whereas the corresponding match is labeled in black on gray background.

One against all alignment for the query motif against all matches found by Fit3D. The residues of the query motif are labeled in green.

Global alignment of the query motif source structure (green) with a structure where a match occurred (grey). The superimposition is based on the matching residues of the query and the target structure. Hence, non-homologous structures can be easily recognized to verify whether a match occurred due to global structural similarity or convergent evolution.

Meta information

Additionally, the toolbox shows information about the query structure when needed (submit a job or extract a motif). Additionally, target lists uploaded by the user are analyzed. When the calculation is finished, some statistics of the results are presented (e.g. intra-/inter-molecular occurrences, maximal/minimal RMSD values). Furthermore, the user can recapitulate the original parameters of the job when inspecting the results.

Submit a structural motif search here. You can either upload a PDB file representing your motif structure or use our extract motif wizard to define a new structural motif. Several algorithmic parameters can be adapted here. If your search should meet some special requirements, check out the advanced settings.

Settings
motif file
Select a file in PDB format as query motif.
target list
Upload target list containing PDB-IDs (and chain IDs) sepearted by line break (see FAQ).
  • none
  • BLASTe-7
  • BLASTe-40
  • BLASTe-80
Choose a pre-defined target list. All predefined lists are provided as download in the help section.
Select the maximal allowed root-mean-square deviation (RMSD) to the query motif (default: 2 Å).
Assign a name to your job.
Enter your email address to be notified when your request is finished.
Click to submit your job.
Click to load example input.
Reset input
Advanced settings