Here is a list of the features included in the current version of Biodesigner. Also, please check the feature tour page. General features Multiple file format support (PDB, Hyperchem, Alchemy, Insight, Sybyl). Automatic recognition of the file type. Native compressed file format BIO. Realtime monitoring of various molecular properties, including distances, angles (bond, torsional and improper), coordinate and distace RMS deviations. 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 out. Molecular builder Atom builder allow for adding and modifying single atoms and bonds. Protein chain constructor can build and alter short polypeptides. Computational engine Superpositioning algorithm Structural alignment of protein chains. Protein chain refinement algorithm. Uses a set of heuristic rules to reconstruct and refine the polypeptide chain. Protein sequence processor Aligning multiple sequences. 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 appliactions. Full integration with molecular viewer window. Any change of the sequence/alignment can be immediately visualized. Changes and bugfixes. Version 0.70 July, 20th, 2002 CASP5 file format supported several memory leaks removed rendering improved in 16-bit modes manual updated Version 0.60 May, 5, 2001 visualization routines entirely rewritten better materials support full-screen mode is now available added support for gzipped input files (e.g. pdb.gz) enabled protein refinement module Biodesigner works now as a single instance program Version 0.60beta February, 7, 2001 added support for native *.bio files added example files added protein chain verification routine added Cut, Copy, and Paste commands added fast manipulation mode added perspective view mode added 'motion blur' rendering mode added 'renumbering atoms' feature much improved control over scene lighting improved rendering routines improved PSI-BLAST support for homology search improved hierarchy window removed several bugs in sequence processor Biodesigner saves AVI files now rather than animated GIFs: faster and more convienient multiple models input routine refined: multiple model PDB files can be read and displayed as animations now program menus cleaned-up configuration file structure cleaned-up Version 0.59 January, 4, 2001 Menus rearranged, various bugs removed, preliminary release before major version number change. Version 0.55 July, 20, 2000 Now the PSI-BLAST program can be used for homology search. Sequence processor has been enhanced. Hierarchy Window displays hierarchy of objects. GetPDB feature allow to load a pdb file just by entering a PDB code. Fixed bug in a pdb file input routine (multiple models were read incorrectly). CHAIN format is now supported. Version 0.54 May, 24, 2000 You can delete selected atoms now Fixed bugs in file output routine Temporary files path can be set now in *.cfg file Now you can select molecules for superimposition POV-Ray rendering is improved a little bit Added materials (visible in POV-Ray images only) Version 0.53 May, 15, 2000 Vast improvements of the sequence processor Added a structural alignment feature Distance map graph can be created Tube and spring models added Improved superimpositoning Labelling has been cleaned up Rendering routine cleaned up Secondary structure calculation routine now works Red/blue glasses support Code cleanup: various minor bugs removed Version 0.52 February, 18, 2000 Registering/unregistering file extensions directly from the program environment 'Set as default' option sets current settings as default settings Setting colors and models works for backbone now as well as for atoms Enhanced animation of models Bug fixed: Biodesigner could work VERY slow when many (>100) molecules were loaded Bug fixed: Program path retrieving worked incorrectly Bug fixed: Number of molecules in world status was sometimes incorrectly displayed Version 0.50 January, 10, 2000 Web-compatible animated GIF file format supported Animation Control Panel changed Bond and torsional angle monitors added Independed support of atom and backbone rendering properties OpenGL rendering bug removed

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