Biodesigner

From MarcsHomepage

Introduction

Biodesigner is a Windows-based molecular modelling tool, intended for homology-building of proteins or DNA. For this purpose, a sequence-editor is included which allows loading and alignment of multiple sequences and modelling of 3-dimensional structures from templates, i.e. a consensus-motif.

Beside this a peptide-chain-building tool and a hierarchical tree-view, like the one found in WebLab Viewer Lite are tightly integrated into the program.

Due to the fact, that Biodesigner is still beta-software, it is quite unstable and produces errors or hangs frequently. Fortunately it does not tend to crash the whole system, so that you may be able to work with it although it is not as stable or usable as for example SwissPDBViewer.

Unfortunately, the program is currently only available for Windows, only a cut-down-version, called TraX (Trajectory eXplorer) is available for Linux and SGI.

User Interface

Biodesigner.jpg

The user-interface is divided into a main window with a button-bar and the usual windows-style pull down-menus and a powerfull, well-integrated sequence-editor as well as the already mentioned tree-view and a chain-building tool.

Selections in one of the main windows are immediately visible on the main screen and vice versa.

Several Features of the program have not yet been implemented, for example the multiple sequence alignment algorithm (only two sequences can be aligned currently, and a protein-chain refinement tool does not work currently

Although the program uses OpenGL for visualization, the online graphics does not look as good as the Molmol or WebLab Viewer Lite-display.

Output can be rendered in Povray, OpenGL-quality or postscript.

Features

Taken from the Biodesigner-homepage

  • General features
  • ** Multiple file format support (PDB, Hyperchem, Alchemy, Insight, Sybyl). Automatic recognition of the file type.
    • Real time monitoring of various molecular properties, including distances, angles (bond, torsional and improper), coordinate RMS, distance RMS, energy.
  • Graphical features
  • ** Various styles of visualization (wire, cylinders, VdW spheres, ball-and-stick, polygon, ribbon, strands, tube, string, cartoon). Possible using several rendering styles in a single picture.
    • Output to bitmap and Postscript formats. Generating raytraced images using external software (POV-Ray).
    • Animation of simulation trajectories. Capability of interpolating of consecutive frames so high frequency molecular moves can be filtered.
  • Molecular builder
  • ** Atom builder.
    • Chain constructor.
  • Computational engine
  • ** Superpositioning algorithm, structural alignment of protein chains.
  • Sequence processor
  • ** Editing multiple sequence alignments.
    • Support for numerous sequence file formats (FASTA, BLAST, PIR, SEQ).
    • Various coloring modes. Includes amino acid identity, similarity, sequence block conservation, amino acid physical properties.
    • Export to Postscript and HTML file formats for publication and web applications.
    • Full integration with molecular viewer window. Any change of the sequence/alignment can be immediately visualized.