In addition to visualization and modeling features BioAdviser implements some very important analysis tools like Compare function, designed for comparisons between conformations of protein chains, Measure facility, that allows for different measurements between atoms of the Molecular structure and Properties Plots that can analyze the structure-activity relations along protein chains. As the special feature, BioAdviser can use MOPAC (MO-G) semi-empirical program (not included in the basic product package) to compute charges and variety of electronic properties of molecules.
- Comparing protein chains
BioAdviser offers the tool necessary to superimpose two selected sections of peptide chains according to RMS criterion. Using this tool the user can create a new system where two peptide chains (target and probe) are superimposed by the requirement that RMS of distances between respective C-alpha atoms is minimized.
- Measurements of atom-atom distance
BioAdviser offers two measurement tools: Atom-Atom pair and mulitlateral. Using these tools the user can measure distances between atoms. The results are displayed on the screen with colored lines representing the distance and/or in “Distances” Edit box from where the data can be transfered to another program. The distance box monitors the atom-atom distances computed by the Measure tools: pair measure (used for individual atom-atom distance) and multilateral measure (used for all atoms captured by a sphere).
- Mapping MOPAC (MO-G) calculated charges on atoms.
- Ramachandran plot.
Ramachandran plots show histograms of distribution of phi & psi angles superimposed on the two dimensional background area with allowed and forbidden sections.
- Protein properties plots:
The value of property can be plotted against aminoacid sequence. BioAdviser offers two general types of plots. In the first type it uses popular QSAR methods like hydrophatic indexes of Kyte & Doolitle, Engelman, Steitz & Goldman or Hopp & Woods. In the second type it uses the internal method where the plot is the weighted sum of other popular methods.
- QSAR methods:
- Hydropathic index (Kyte & Doolitle).
- Hydropathic index (Engelman, Steitz & Goldman).
- Scaled hydrophobicity.
- Hydropathic index (Charge).
- Hydropathic index (Hopp & Woods).
- Internal methods:
- Karplus and Schulz.
- Hopp and Woods.
- Kyte and Doolittle.
- Robson and Garnier.
- Aminoacid sequences.
Uses symbols of 3-letter or 1-letter aminoacid codes. The elements of secondary structure may also be displayed between boxes representing aminoacids.