Protein modelling on Macintosh

Jean-Claude JESIOR jean-claude.jesior at imag.fr
Wed Jul 13 00:28:08 EST 1994


Release of 'FoldIt (light)' v.3.7.3 (freeware)
Author: 
   Jean-Claude JESIOR
   TIMC (URA D1618), CERMO, BP 53, 38041 Grenoble Cedex 9 (France)
   tel: (33) 76 51 48 13             fax: (33) 76 51 49 48
   e-mail: jean-claude.jesior at imag.fr

WHAT 'FOLDIT (LIGHT)' DOES?
'FoldIt (light)' is a molecular modelling program to visualize and
manipulate proteins. 'FoldIt (light)' is an interactive program with a user
friendly interface. The goal of this program was to build an integrated
environment in which statistical analysis as well 3D observations could be
realized on PDB files without having to transfer files or swap machines.
Our major underlying research project is still to try to improve the
folding prediction methods (hence the name 'FoldIt'). This is also the sole
desactivated feature in this released version (hence the adjective
'(light)').
'FoldIt (light)' is intented to provide the possibility to analyze proteins
up to 2000 residues in size, to visualize and manipulate them
interactively. It can directly read any protein coordinate text file from
the Brookhaven Protein Data Bank (PDB) (Bernstein et al., 1977) including
hetero-atoms and water molecules.
'FoldIt (light)' has two main windows: a color image window to display the
protein structure and a text window to record the result of all operations
requested by the user.
The protein structure can be manipulated easily in real time with the
mouse, zoomed or observed in stereo. Structure movement can also occur
stepwise for a more precise control. Animations can be created.
Steric conflicts, disulfide bonds, hydrogen and ionic interactions can be
located and displayed in the protein structure. These interactions are also
reported in the text window.
Atoms and residues can be tagged individually (or globally) and structural
information can then be extracted.
Portions of a structure can be read into memory or displayed.
Two structures can be read at the same time in memory and can be overlapped
automatically.  The second structure can be manipulated independently of
the first.
Bonds can be rotated and atomic parameters can be changed.
The sequential folding of a protein can be simulated.
It is possible to create a protein de novo from the menu or by entering the
sequence from the keyboard. Structures can then be manipulated locally or
forced into helices.
The application can process structures in the batch mode to extract a
number of structural features: Ramachandran plots, SS-bond plots, H-bond
plots. Statistics on atomic parameters are displayed as histograms.
The content of image and text windows as well as histograms can be saved to
disk.

SOFTWARE ENVIRONMENT
'FoldIt (light)' can only work on Macintosh computers running under system
7.0 and above.
It has been developed with Symantec Think Pascal and includes 37000 lines.
The application can run in the background which is convenient for lengthy
statistical procedures. 'FoldIt (light)' does not support printing but can
save the content of its text window (report of different operations and
data analysis) and the content of the image window (result of graphic
operations) in TEXT or PICT formats. These files can then be manipulated by
other specialized applications and printed. 

HARDWARE ENVIRONMENT
'FoldIt (light)' runs on any Macintosh computers equipped with 68030 (+
coprocessor) or 68040 microprocessors (i.e. Macintosh SE30 to Quadras). The
application itself requires 684KB of memory and 4.5 KB of additional memory
for each read residue: this means that 900 KB of extra RAM are necessary to
read a typical 200-residue protein. Color monitors are preferred to give a
better depth perception but black & white monitors may also be used.

DOCUMENTATION
An in-line documentation is included as desk accessory. Several small size
protein structures are included as example.

The protein modelling program 'FoldIt (light)' is available by anonymous
FTP at: brise.imag.fr (129.88.110.7) in directory /pub/mac/programs.
Please contact the author (Jean-Claude JESIOR) for comments at the
following address: jean-claude.jesior at imag.fr




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