Manual
1. Introduction
2. Program Window
3. User Interaction
3.1 Menus
3.2 Keyboard Button Actions
3.3 Mouse Button Actions
4. Sequence Alignment
5. Internal Residue Calculations
6. Secondary Structure Prediction
7. Least Square Fit - LsqFit module
8. Model Construction - Franky
9. Installation
HoMo is a homology modeling program for protein macromolecules. It includes modules for sequence alignment, secondary structure prediction, least square fitting of tertiary structures and construction of models. As input accepts aminoacid sequence files in FASTA and PIR format and PDB files. The output is always the 3D structure of the predicted molecule in PDB format. For the construction of the target molecule multiple protein sequences can be used as templates. The user manipulates the sequence and selects options though a visual editor window in the form of a Java applet.
The sequences with all the additional information (like secondary structure
predictions, internal residues and user selections) are displayed in an
applet window.
Internal residues and secondary structure predictions are displayed
below each sequence. The residue colors and their relevant information
can be customized by the user.
Most of the sequence manipulation and the activation of different molecules
is taking place through menu selections. A brief description of them appears
at the bottom of the editor window as they get selected.
3.1 Menus
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File
Menu : Basic input - output operations
Edit:
Sequence manipulation and selection of program variables
Display
: Selection of display information
Run
:
Execution of modules on the server
Help
: Information in English and Greek
3.2 Keyboard
Button Actions
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Arrow keys : Move cursor within sequences
Home
: Move to the beginning of sequence
End
: Move to the end of sequence
Page
Up : Move to the first sequence
Page
Down : move to the last sequence
Insert
: Inserts space at current position
Delete
: Delete space at current position
Backspace
: Delete space to the left of current position and advance cursor to the
left
Shift
+ Left or Right Arrow : Underline - De underline residues for model
construction
F5
: Select columns as references for least squares fitting
F9
: Select target sequence. All alignment information is referenced according
to the
target sequence. Reselect to cancel. Same effect can be achieved through
menu selection -
Edit - Target
#,
~ : Marker symbols. The user can use them to specify residues with
special
characteristics like active center residues.
3.3 Mouse Button
Actions
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Left
Mouse Button
Click : Move cursor to pointer position
Press + Hold + Drag : Underline - De underline residues for model construction
Middle
Mouse Button Click : Inserts space at current position
Right
Mouse Button Click : Delete space at current position
At present CLUSTALW is executed on the server and the results are presented in the program window.
This module calculates internal residues. The molecule space is divided in identical cube cells. The user defines the cube dimension and the module marks with the letter "i" all the residues that are surrounded along the coordinate axes with filled cells.
The methods of Chou and Fasman, Burgess, Garnier, Lim and Kimura are implemented.
A grid method is used for the 3D alignment. The user selects (by pressing
F9) a minimum of 4 columns from the program window. The Ca coordinates
of the selected residues are used for the evaluation of the 3D fit based
on the least squares criterion.
The geometric center of the selected Ca atoms is used as reference
point. The module initially transfers the 3D structures so as to coincide
all geometric centers. It continues with rotations and translations covering
the conformation space of the possible orientations. It progresses from
large steps to smaller until convergence.
The user selects aminoacid chain fragments (by underlining) from the known structures. Initially a skeleton is constructed by adopting the aminoacid chain coordinates of the selected fragments (from their PDB files). Then the side chains are constructed by adopting the coordinates of the common atoms between the side chain atoms of the known and target proteins at every residue position. The remaining atoms for the completion of the target molecule side chains are added by adopting the most frequently observed conformations. The module also refines the structure by relaxing the bonds of conflicting conformations. At this stage only rotations are performed.
You need Java Plug-in 1.2 and above to view the applet.
Download from http://java.sun.com/products/plugin/old.html
Also you need to download the policy file Policy
and copy to:
Solaris : your home directory
Windows : C:\WINDOWS
This will allow the applet to read input files (PIR,FASTA,PDB and Work)
for your local drives.