Modules currently running in DAM-Bio

Click the button to read documentation about the desired tools in a separate window, or the to access the tools' homepages. Then roll down the page to proceed...

II. Structure related tools

Homology modeling program for protein macromolecules: The following modules are included:
  • Sequence alignment: Multiple sequence alignment may reveal conserved regions that could be used as a template to model an unknown structure.
  • Secondary structure prediction: Reliable predictions of local structural elements may be used to guide the modelling procedure.
  • Least square fitting of tertiary structures: Fitting known tertiary structures indicates structurally conserved regions and rigid segments to be used in the modelling step.
  • Construction of models: Build a model from selected parts of known structures followed by an optimization step.
As input accepts aminoacid sequence files in FASTA and PIR format and PDB files. The output is always the 3D structure of the predicted molecule in PDB format. For the construction of the target molecule multiple protein sequences can be used as templates. The user manipulates the sequence and selects options through a visual editor window in the form of a Java applet. 		Mirror 1:

 

Mirror 2:

 
Structure Representation: S.C.A.R was developed to create, display and manipulate structures of small molecules, proteins and DNA.

Least Squares Fit of 2 or more 3d-structures: LSQR was developed to optimise by a least squares method the fit of a subset of atomic coordinates from one file (assigned to workcd) to the same subset of coordinates of another file (assigned to refrcd). The program can also give the same statistics of fit (e.g. rms differences between atom pairs,etc) without any transformation of the working coordinates.

Proceed

Greek version
Back to DAM-Bio Homepage
Back to Biophysics Lab
Comments: liakop@biol.uoa.gr