A GUIDE TO INTERNET SOURCES FOR MOLECULAR MODELING

The Internet has an incredible variety of resources that could be useful to you in this class.  One such resources is the National Institute of Health.   You can get to this resource by a variety of ways through Netscape.  From Netscape, click on NET SEARCH in the lower menu bar at the top of the window .   Scroll down the page and click on LYCOS HOME PAGE:  HUNTING WWW INFORMATION.   Type in NIH and you will be given multiple "hits" that most closely match NIH.Click on next ten hits to select WELCOME TO THE NIH.   Keep clicking until you get to the NIH HOME PAGE.  Click on Scientific Resources, then Molecular Modeling Home Page.Click on Knowledge and Onramp to get an unbelievable amount of useful information. They have recently removed one of the best narrative descriptions of molecular mechanics and dynamics I have found, but I hope they restore it soon.
                                                 
Under knowledge you will find links to such topics as:
     a.  NIH Guide to Molecular Modeling
     b.  docking tutorial
     c.  organic chemistry resources
     d.  molecular modeling
     e.  molecular graphics
     f.  Quanta Tutorial I and II.
    

ACCESS TO PROTEIN STRUCTURE FILES
The table on the next page shows a list of files containing protein structure coordinates.   These were determined by X- ray crystallography and were deposited in the Protein Data Bank of Brookhaven National Labs.  These files are available in read-only files in the directory /usr/people/chem/students/proteins.  They will be useful to use for the first two bulleted applications at the top of this document.  However, after you have used these files in Quanta/Charmm, you will be prompted to save the files.  I encourage you NOT to save these protein files if you don't need them since they will just fill up disk space.  You can always get to these protein files anytime.  You can get access to ANY PDB protein structure file through the INTERNET.  The easiest way is to go to the CH331 home page. Click on A guide to some useful internet resources for - THE GENERAL COURSE  and then in the Molecular Modeling Section, select: Downloadable protein and nucleic acid structures for use with Quanta/Charmm from the- BROOKHAVEN NATION DATA BANK .
Once there, add this location to your bookmark list. Select an almost full text search .....  Then you will be prompted to type in the name of a protein as a keyword.   For instance, type in trypsin, and a whole list of different PDB trypsin structures files will be displayed.  Click the one you wish, and you will be prompted with a choice of three files:

• file.biblio  a brief summary of the protein file
• file.full  - contains the coordinates for the protein
• file.gif  -  displays a quick structure of the protein.

If you wish, save the filename.full file it to your home directory as prompted.  You can not use these files directly in Quanta/Charmm.  The pdb files have only the coordinates for the atoms, and do not have connectivity among the atoms. Quanta/Charmm can read the coordinates, but must generate
connectivities in a separate step.  For files that you bring in from the Internet, you must use the
     File
          Import
commands, not the File, Open,  commands.  The program will ask you several questions before the file is saved.  Answer yes to all questions.  When prompted a file name, use the 3 number/letter code of the pdb file, along with your choice of identifiers, for the file name.  Quanta will automatically append as a suffix a .msf to the file name, where msf stands for molecular simulations file. You can use all the files that I have set up in an account called CHEM331PROTEINS.  This is a read only account, from
which you can copy to your own directory. 

An important set of new instructions to downloading a pdb file to your m: drive.: 

From the networked PC's:

Go to the Protein Data Bank and find your file.  Then select Download/Display File from the menu on the left.  Then select from Display the Structure File, PDB file format, complete with coordinates and text.  The pdb file will display as a text file.  Highlight the entire file with your mouse, copy it by typing ctrl C, and then paste it (ctrl V) into Notepad  (opened by gong to Network Programs, Windows Systems Applications, Accessories, Notepad.  

From the SGI's:

Go to the Protein Data Bank, select your file.  Then select Download/Display File from the menu on the left.  Then select from Download the Structure File, PDB file format, no compression.  Then email this file to your PC account by going into Application, Media Mail, Compose New Message, to which you must select Attach and select the pdb file for attachment before you send it.  Save the file to your m: drive as a pdb file. That's all there is to it!

A direct way:

A better and more direct method is to simply map your Unix files to your PC. Go to IT's  Information Page:
Windows to Unix Connectivity

From the SGI's:

Old instructions if you have trouble:

Follow the directions above and save it to your Unix account. Next you must do a few extra things.

•  In the blue Unix shell, type the following at the prompt: chmod a+r xxx.pdb
  where xxx.pdb is the name of your pdb file (i.e. change the xxx to whatever the first part of your file name is). This will give the correct permissions to the file. 
• Next open Media Mail. From the top menu bar select compose new. A new window pops up. Type in your email address in the TO box. Next follow the prompts to Attach a File. You will have to click on the file you wish to attach and then click attach and then close. A text file icon will appear in the attachment window. Then send the message. Go to your PC mail and open the file. The PDB file will appear as a text file. Select from the top menu bar, File, Save As, and follow the prompts to save it to your m: drive. SAVE IT AS A .TXT FILE, not a .RTFfile. Then go to Windows Explorer, and change the extension to .pdb from .txt.

NEW 4/28/99!

PROTEIN DATA BANK - SOURCE OF INFORMATION ABOUT ENZYME

The   Protein Data Bank   has just moved to a new site (click the hypertext).   Once there, select Search and then enter a string describing your macromolecule as described underneath the string box.  After the search result come back, click on the red Explore icon to the right of the file name. A summary information sheet appears, with a series of options available to the left:

View Structure:  Will allow you to interactively view the molecule if your browser can read VRML - virtual relaity markup language.  This is a plug-in for Netscape

Download/Display File:  Allows you to download PDB files

Structural Neighbors:  Gives result of the following analyses:

• CATH: Class, Architecture, Topology and Homologous superfamily - a hierarchical
  classification of protein domain structures;
• CE: Combinatorial Extension of the optimal path, Research Collaboratory for Structural Bioinformatics (RCSB) Features: Complete PDB and representative structure comparison, structure, alignments, structure superposition tool
• FSSP:Fold classification based on Structure-Structure alignment of Proteins ,European Bioinformatics Institute (EBI) Features: Complete PDB, fold tree, domain dictionary, sequence neighbors,structure superposition
• SCOP: Structural Classification Of Proteins, MRC Laboratory of Molecular Biology and Centre for Protein Engineering . Features: Augmented manual classification, class, fold, superfamily and family classification
• VAST :Vector Alignment Search Tool ,National Center for Biotechnology Information (NCBI); Features: Complete PDB and representative structure comparison, structurealignments, structure superposition tool
  

Geometry:  Shows a table for dihedral angles, including average phi, psi angles along with minimum and maximum angles.

Sequence Detail:  Give the amino acid sequence and other information

Using your browser, go back to the search results window.  Go to Choose from the followng options, scroll down the list, and select Create a Tabular Report.  From the next page, select one of the following:

• Primary Citation-primary bibliographic citations
• Structure Identifier- identifiers and descriptor
• Sequence- strand ID, sequence, and strand length
• Nucleic Acid Sequence -strand ID, sequence, and strand length for nucleic acid strands only
• Protein Sequence -strand ID, sequence, and strand length for protein strands only
• Experimental Technique- descriptor and experimental technique