Software for molecular modeling has to incorporate certain basic facilities. These include (1) ways of inputting the structure(s) to be worked with, (2) means of storing and outputting structures and the results of calculations, (3) computation and manipulation of the "conformational energy" of structures and systems of structures, (4) ways to incorporate the effects of solvent, and (5) methods for simulation of molecular dynamics. Particular programs differ in the ways in which these features are provided and in facilities for additional, more sophisticated calculations. Three commonly used commercial software packages having these features are MacroModel, SYBYL, and Insight/ Discover. All of these are available in the laboratory.
MacroModel is oriented toward studies with organic molecules as well as biological structures. It is largely a product of Clark Still's group at Columbia and is available at low cost to academic groups. It is marketed by Schrodinger, Inc. (www.schrodinger.com/index.html). MacroModel supports a wide variety of force fields including the Allinger MM* force fields and versions of the AMBER force field. A continuum solvation model is implemented in the program. An on-line manual for MacroModel is available at www.schrodinger.com/MacroModel/userman/userfram.htm.
SYBYL is a product Tripos Associates (www.tripos.com) and can be used for modeling organic, inorganic, and biological molecules. A BIOPOLYMER add-on supports work with biological structures. The system is particularly oriented toward drug discovery; a variety of force fields is available.
Insight/Discover is part of a complex set of programs and capabilities available from a firm now called Accelerys (formerly Molecular Simulations, Inc., (http://www.accelrys.com/insight/ Insight2.html). The package is particularly strong in supporting calculations with repetitive structures and molecules in different phases.
There are many other software packages available that may offer certain advantages. Among the commercial efforts are AMBER (www.amber.ucsf.edu/amber/amber.html), HYPERCHEM (www.hyper.com) and MOE (www.chemcomp.com). Quite good programs are available as freeware, often with the source code being made available. Among the latter are TINKER (dasher.wustl.edu/ tinker) and AAMP (asterix.jci.tju.edu). Some of these are designed to run on PC or Mac systems.
The exercises for this course make the assumption that the program SYBYL, run in the departmental computation laboratory, will be used in completing them. This is not a requirement. Use any modeling/simulation software running on any system that you feel comfortable with, but be sure to indicate in your reports what package was used.
Set up your own modeling system?
Have your own computer at home? You might consider setting up your own facilities for viewing molecules in various renderings and for carrying out the calculations used in the exercises.
Activity: (1) Download the HIV protease structure (1HVH.pdb) from the Protein Data Bank and store this in your directory labeled exer2. (2) An introduction to the use of SYBYL for modeling small molecules and biological macromolecules is attached. Work through this to become familiar with the basic modeling capabilities of the software. Create a ball-and-stick rendering of the DNA fragment and annotate it with your name and a catchy title. Obtain a hard copy of the display, including in one frame the molecule, your name, and the title. (3) Measure the distance between the distance between the C? of amino acid 12 and C? of amino acid 28 in HIV protease. Measure the dihedral angles phi and psi at residue 28.
Optional: There is a function (ProTable) available in SYBYL which will determine several properties or aspects of a protein structure, including detection of backbone dihedrals and the calculation of the hydropathy of the sequence. This function is available under Biopolymer -> Analyze Protein (ProTable). This function would provide an alternative way of getting some of the information requested above. You may wish to examine the SYBYL tutorial on "molecular spreadsheets" (databases) before running ProTable.
Return to the
top of this page.
Responses to the following questions and the hard copy indicated above are to be turned in by January 25.
(1) How many base pairs are represented in the "Dickerson dodecamer" structure?
(2) What were the distances and angles determined for HIV protease?
Return to the
top of this page.
An Introduction to the SYBYL Molecular Modeling Package
SYBYL/Base is the heart of Tripos' software suite. Touted as a "comprehensive computational tool kit for molecular design and analysis", SYBYL/Base provides essential construction and analysis tools for both large and small molecular structures. The program provides facilities for building, superimposing, geometry optimization, distance geometry, docking, and interfaces to quantum mechanical and other methods.
The Biopolymer module provides for specialized treatment of macromolecular
structures and systems.
ComposerTM, MatchMaker and GeneFold all provide different approaches
to the problems of Protein Folding, Sequence, and Structural Similarities.
ProTable enhances the SYBYL "Molecular Spreadsheet" for the analysis
of protein structural integrity.
The GASP, RECEPTOR, and DISCO modules provide techniques for conformational searching and for pharmacophore recognition and analysis.
Quantitative Structure Activity Analyses is supported by the QSAR, Advanced CoMFA, and HQSAR modules.
FlexX and FlexiDock allow investigation of the configurations necessary for ligand binding to protein receptors.
These modules and several more are described in more detail at the
Tripos website: http://www.tripos.com/software/index.html.
This series of exercises is intended to introduce you to SYBYL. Most
of the modules from Tripos use this program as a platform from which to
launch other kinds of simulations or modeling.
To start the program, open a Unix Shell window and type sybyl at the Unix Shell command line. It will take a few moments for the program to come up completely. It will probably be convenient to have Netscape running in another window since documentation for the various Tripos modules can be accessed though the web browser.
There are several things to notice about the SYBYL screen when it first comes up. The first is the list of menu names horizontally arrayed across the top. Second is the column of icons at the left edge. The third icon provides a means of quickly changing the display mode (ball-and-stick, space-filling, and so forth). The fifth icon allows adjustment of details of how molecules are rendered, including selection of colors for the molecular components and the background. The icon with a cross in it permits rotations and translations about each Cartesian axis. All of these left-column icons remain displayed once they are clicked on until the Q (for quit) button in the icon window is clicked. You can explore the functioning of the remaining buttons is this column at your leisure.
The Unix shell window that you started SYBYL from remains open and becomes the text window for the program. Output from the various program functions will appear here and commands for SYBYL can be entered here when the SYBYL prompt (Sybyl>) is present.
The z-axis of a drawing in perpendicular to the screen and the x and
y axes lies in the plane of the screen. You can also zoom and rotate by
using combinations of mouse buttons. By default:
the left mouse button selects atoms;
the right mouse button rotates the structure around the x and y axes
(when the mouse is
dragged;
the middle mouse button translates the structure in the x and y directions;
the CENTER+RIGHTcombination of mouse buttons is used for zoom (or scale
changes);
the LEFT+RIGHTcombination of mouse buttons is used for rotations about
the Z axis.
RUN A TUTORIAL
Using the web browser, find the tutorial for sketching small molecules that is given in the Tripos Bookshelf. (An abbreviated print version of this tutorial is attached.) Work through this tutorial.
Note that there are tutorials available for many of the functions of SYBYL. Most of the elements of this exercise will use the Biopolymer module, which is accessed by clicking Biopolymer in the top menu bar.
Return to the
top of this page.
GET A STRUCTURE
Click on Biopolymer to bring up the choices on this menu.
Click on Build, then DNA strand, then click on Cancel. (This sets up
parameter files that are appropriate for nucleic acids.)
Click on Brookhaven File, then READ.
SYBYL lets you have a number of molecular structures present simultaneously.
These are held in "molecular areas" labeled M1, M2, …. Select M1
to hold the first molecule by clicking on this. The Brookhaven file menu
comes up.
Specify the directory path to the PDB file containing "Dickerson's
dodecamer" that you created previously. Click on the file name.
SYBYL will ask about centering the molecule. This is generally desirable
since rotations take place about the geometrical center of the structure
and are therefore more likely to remain in view on the screen.
Zoom and rotate so that the entire DNA fragment is displayed in the
drawing window. The drawing may appear faint or may partially disappear
in this process. This is because the z-clipping is set inappropriately.
To adjust z-clipping, click on the eighth icon from the top on the vertical
array of icons on the left side. Choose ZClip Everything and change the
width and mid-point of the z-slab by clicking on the increase or decrease
arrows until the display is satisfactory.
You should now have the wire frame structure of a DNA fragment displayed
in the SYBYL drawing window.
WRITING A STRUCTURE
To write a structure file in PDB format, go to the Biopolymer menu,
select Brookhaven File, then Write. Supply the name of the new file (without
any extension) and click OK. The file will be written with the specified
name and the extension .pdb.
SELECTING ATOMS, RESIDUES AND MOLECULES
Several functions controlling the nature of the molecular display require selection of all or part of a structure. In these instances, three menu buttons will come up (as part of a larger menu): Sets, Atom Types and Substructures. SETS are reasonable groupings of substructures such as sidechains or backbone. Some are built-in, others are defined because of the nature of the molecule, and still others can be defined by the user. One or more sets can be selected by clicking on the small box next to their name or by clicking on their name in the list provided. The Atom Types menu can be used for selection of certain atoms in a structure, for example all aromatic carbon atoms. Substructures are the amino acid or other subunits that make up the biopolymer. These are listed in the order in which they appear in the primary sequence. A particular subunit is selected by clicking on its name, followed by OK. Finally, simply positioning the cursor on or very near the atom on the screen and clicking can make selection of individual atoms.
After a selection by any of these methods has been made, small squares or diamonds on the displayed molecule will mark the atoms selected. (The Highlight option has to be switched on; being on is the default setting.) If a mistake has been made, a selection can be undone by clicking on Undo and then OK. There is also a facility for clearing all selections.
Boolean combinations for selections are possible--click the button labeled Union to implement one of these. The Invert button selects all of those atoms not selected by previous selection methods; clicking Invert twice gets you back to the original selection.
Return to the
top of this page.
CONTROLLING THE DISPLAY
Coloring by atom type
Click on View >>> Color >>> By Atom Type.
Coloring atoms in other ways
Click on View >>> Color >>> Atom…
A selection menu comes up. Select the atoms to color. For this example,
select Sets, then Purine. Click OK. You should see the purine residues
marked with diamonds. Click OK. Now a color choice menu comes up. Select
a color and click OK. Now the purines are rendered with that color.
Changing how the atoms are displayed
The simplest way to change the way a structure is displayed is to click on the third menu item from the top in the left-hand vertical column. You can select the rendering method (Space Fill, Ball & Stick, Stick or Lines) there. Examine each of these renderings of the DNA structure. Note that attempting to rotate or translate any rendering other than Lines has a slow response, very slow in the case of the Space Fill rendering.
For a more selective application of a rendering method click on View
>>> Mixed Rendering… Select the kind of representation to be used from
the list that comes up. Chose one of these and click OK. Now a selection
menu comes up. Choose the Pyrimidine set and click OK. (You should see
the pyrimidines of the DNA structure marked with diamonds. Click OK and
the pyrimidines will be rendered with the selected method.
To get back to a simple wire frame display of the DNA molecule, click
View >>> Delete All Backgrounds.
Calculate and display the hydrogen bonds
Add hydrogen to the structure: click Biopolymer >>> Add Hydrogen… >>>
All >>> OK. Select to add ALL hydrogens when asked.
Click View >>> Display H-Bond >>> Static.
Another selection menu comes up. Choose All and then OK. Finally, another
menu comes up for selection of the color of the dotted line that will represent
the hydrogen bond. Choose your favorite and click OK. Hydrogen bonds between
the base pairs of the DNA should now be rendered by dashed yellow lines.
Note that one could have different types or classes of hydrogen bonds colored in different ways by repeating this sequence and making different selections.
Clear display of H-bonds
To erase the hydrogen bonds and get back to a simple wire frame display of the DNA molecule, click View >>> Delete All Backgrounds.
Now delete the DNA molecule by the sequence Build/Edit >>> Zap (Delete)
Molecule.
Click Biopolymer >>> Build >>> Protein. Then click on Cancel. Read
in the PDB file for the HIV protease structure (1HVH.pdb). Color the drawing
according to atom type.
Examine folding using a ribbon figure
Select Biopolymer >>> Display >>> Shaded Ribbon.
Another selection menu comes up. The various ribbon displays possible
are listed; select Shaded Ribbon...
Click on Chain A then drag with the left mouse button depressed until
the entire chain A sequence has been highlighted. Click OK. (The ribbon
will eventually be drawn through only the A-chain of the structure.)
Now a menu for selection of the ribbon color appears. Choose a color
and the click OK.
The process can be repeated in order to create and color a ribbon or other rendering of Chain B of the HIV protease structure.
To remove the display of the individual atoms, View >>> Undisplay Atoms …. >>>. Then select All and OK from the selection menu that comes up. One could at this point choose to undisplay only a part of the structure.
Clear display of the ribbon
To erase both ribbons and get back to a simple wire frame display of the HIV protease dimer, click View >>> Delete All Backgrounds. If you want to remove only one of the ribbons, click View >>> Backgrounds >>> Delete. A listing of the various ribbons (renderings) that have been made appears and a choice can be made regarding which one(s) to remove.
Display a van der Waals molecular surface
Select View >>> Dot Surfaces… >>> vdw Dot Surface…. Select the atoms which will be surrounded by the dots representing the van der Waals surface and then select the color to be used for the dots.
Notes: (1) In SYBYL the dots for a dot surface are stored in a file and retained as a "background" which can be turned on and off or re-colored in the same way that ribbon or other representations are retained and manipulated. There can be several dot surface files for the same or different parts of the molecule and these can be colored as one wishes.
(2) The density of dots per square Angstrom is set at 12. This density can be changed through the use of the "tailor" function in SYBYL. Click Options >>> Tailor >>> Set >>> DOTS >>> DENSITY to get a menu that will let you change this parameter.
(3) There is considerable computation involved in producing "dot surfaces". Be prepared for a delay when creating a dot surface for a large molecule.
Return to the
top of this page.
ANALYZING A STRUCTURE
Measure selected bond lengths and angles
Select the Analyze menu, then Measure.
Note the different possibilities for "measurement". Select Distance.
This function will report the distance between two atoms. The atoms
may be selected by typing their names at the appropriate line in the menu
that comes up or, more conveniently, just by pointing and clicking the
left mouse button. After selection the distance between the atoms selected
appears in the window where SYBYL was started.
List bond distances or angles
Select Analyze >>> Measure >>> Topography.
Select the class of parameter to be listed from the menu that appears
and click OK. Now a selection menu comes up and one can select for which
part of the structure the selected parameter will be listed. After clicking
on OK a listing of the requested information appears in the window where
SYBYL was started.
HARDCOPY OF DISPLAYS
To place annotations on the screen display click View >>> Annotation. The menu that comes up will let you place text and arrows on the screen display. These will be printed on hardcopy.
To make a hard copy of the screen and annotations created Click File >>> Print >>>Screen Capture. Set the options to PostScript and Grayscale Image. Enter a file name with the appropriate path and with the extension .ps. Click on Create&Close. You can print the file with the lp command. It is recommended that the image contained in a .ps file be examined with the SGI utility xpsview before printing.
Notes: Several formats for the image files created are available. Some
of these should be readable into word processing programs. There is a tutorial
on preparing hardcopy. Set the web browser to open /usr/local/spec/ sybyl/TriposBookshelf/sybyl/graphics/Output/graphics_tut23.html#13323.
EXIT SYBYL
To leave the program, make sure to save any data that you wish to retain.
Then click File >>> Exit SYBYL.
HELP
There is extensive documentation available from Tripos for SYBYL and
its associated modules. To view this on the CCBL system, open Netscape
and then open the (local) file /usr/local/spec/sybyl/ TriposBookshelf/sybyl/index.html.
to view the index to the Tripos written documentation. (You will probably
want to add this URL to your Bookmarks in Netscape.) Alternatively, click
on the Help button at the upper right of the screen and choose Start Browser.
When Netscape is running, return to the Help menu and select Start Bookshelf.
There are tutorials for many modules available. Tutorials and documentation
may be accessed through the web browser or obtained as printable (PDF)
files.
Preliminaries. Download the structure file 1BPI from the Protein
Data Bank. This contains the structure of bovine trypsin inhibitor (BPTI),
a peptide inhibitor of trypsin and other proteases. Open this file in the
text editor. Note that the coordinates for hydrogen atoms are not found
in this file (Why not?) and that a number of water molecules and other
species are distinguishable by the crystallographic experiment. Edit the
file to remove the coordinates of the water molecules and these other species.
Store the edited file under the name 1BPI-water.pdb.
1. Read through the attached tutorial for the program MacroModel and try the various operations described therein. When you are somewhat comfortable with these open your 1BPI-water.pdb file. Use MacroModel to determine and write on the screen what is the distance between the Ca of amino acid 12 and Ca of amino acid 23 in BPTI. Plot the screen to a PostScript file (.ps extension) and print that file. Set up the title line so that it includes your name. Turn in printed output which shows the region of the structure containing these amino acids and the distance mentioned.
2. Read through the attached handout about using Insight II and then try the exercises described therein. Delete all molecules and read your 1BPI-water.pdb file into the program. Create a ribbon display of BPTI from this data and obtain a hard copy of the display (without the wire frame structure showing). Determine the conformational angle f for residue 17 and place this on the hard copy. Turn in this annotated hard copy as part of the report for this exercise.
3. Work through the attached handout about using SYBYL. Clear the display and read your 1BPI-water.pdb file into the program. Create a ball-and-stick rendering of BPTI and annotate the rendering with your name and a catchy title. Obtain a hard copy of the display. Measure the distance between the distance between the Ca of amino acid 12 and Ca of amino acid 23 in BPTI and write this on the printed copy. (Same answer as obtained with MacroModel?)
Turn in the hard copies prepared stapled with a cover sheet that includes your name.