Computational Tools
Here you find some software tools:
- The 3D hydrophobic moment vector calculator allows you to calculate hydrophobic moments based on the electrostatic potential on the molecular surface. The resulting vector is three-dimensional and points towards the most hydrophobic parts of the surface. It can be used e.g. to qualitatively predict the insertion behaviour of an amphiphilic peptide into a membrane. The method is applicable to arbitrarily shaped molecules and requires a PDB or PQR (coordinates, charges, atomic radii) file as input. Additionally, peptides which are predicted to be helical can be entered as amino acid sequence and will be treated like ideal alpha-helical peptides.
S. Reißer, E. Strandberg, T. Steinbrecher, A.S. Ulrich. 3D hydrophobic moment vectors as a tool to characterize the surface polarity of amphiphilic peptides. Biophys. J. 106, 2385–2394 (2014). DOI: 10.1016/j.bpj.2014.04.020 (Please cite this reference when using the software for academic publications.)
Run the 3D Hydrophobic Moment Vector Calculator online - Protein Origami
The 3-dimensional structure of a protein or a peptide often is quite important for its biochemical behavior. Nevertheless its spatial appearance is hard to imagine, especially for an untrained person. Protein Origami wants to simplify this by assisting the user in visualizing amino acid sequences in different ways and constructing 3-dimensional paper-models of it.
S. Reißer, S. Prock, H. Heinzmann, A.S. Ulrich. Protein ORIGAMI: A program for the creation of 3D paper models of folded peptides. Biochemistry and Molecular Biology Education 46, 403-409 (2018). DOI: 10.1002/bmb.21132 (Please cite this reference when using the software for academic publications.)
Run Protein Origami online