Volume 2 Chapter 10 Search Menu PDB-SEARCH

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PDB-SEQUENCE

Function

The PDB-SEQUENCE sub-menu is used to construct sequence based searches of the Brookhaven Protein Data Bank (PDB) entries, all of which have been converted into the QUEST ASER search format.

Basic QUEST Procedure

The equivalent test construction in Basic QUEST is discussed under *PDBSEQ.

It should be read carefully before using the Graphics QUEST3D interface.

Graphics QUEST3D Procedure

The PDB-SEQUENCE sub-menu is shown below.

This table summarises the buttons in the PEPTIDE-SEQ sub-menu.


                      Function                                                       
Button                                                                               

PDEF                  Begins the specification of a user-defined amino acid group    
                      ("Peptide Definition").                                        
                      If a red box is displayed around this button, you are          
                      currently in the middle of building a "definition" of a new    
                      amino acid type, and the prompt in the dialog area will show   
                      the allowed amino-acids; otherwise, you are a building a       
                      "sequence" of amino acids which will constitute your test,     
                      and the prompt in the dialog area will show the sequence thus  
                      far.                                                           

+                     Specifies that subsequently selected amino-acids are to be     
                      added to the definition.                                       

-                     Specifies that subsequently selected amino-acids are to be     
                      subtracted from the definition.                                

=                     Declares that the current PDEF is now complete.  The           
                      newly-defined group is shown in the "USER-DEFINED" section of  
                      the menu, and may now be included in the sequence.             

NON-STANDARD-CODE     Prompts for an amino-acid or heterogen 3-character code, to    
                      be added to the current sequence.  The list of all known PDB   
                      codes is searched, to ensure that a valid code was entered.    

LEFT-END              Sets the allowable bonding pattern at the left hand end of     
Terminal[%]           the sequence.                                                  
Non-terminal[-]       Turning off both options is equivalent to selecting just       
                      Terminal[%].                                                   
                      On first entering this sub-menu, both these options will be    
                      turned on.                                                     

RIGHT-END             Sets the allowable bonding pattern at the right hand end of    
Terminal[%]           the sequence.                                                  
Non-terminal[-]       Turning off both options is equivalent to selecting just       
                      Terminal[%].                                                   
                      On first entering this sub-menu, both these options will be    
                      turned on.                                                     

EXHAUSTIVE_SEARCH     By default, QUEST will only locate the first occurrence of     
                      the given sequence in each entry in the database.  By turning  
                      on EXHAUSTIVE_SEARCH, QUEST is instructed to find every        
                      location of the target sequence.                               

NO_OF_CHAINS          If this command is used, QUEST will only search entries with   
                      number of chains in a given range.  For example, you may say   
                      that the number of chains must be "> 3".                       
                      The recognised symbols are:                                    
                      <> or .NE. "not equal to"                                      
                      =  or .EQ. "equal to"                                          
                      <= or .LE. "less than or equal to"                             
                      <  or .LT. "less than"                                         
                      >= or .GE. "greater than or equal to"                          
                      >  or .GT. "greater than"                                      
                       Ð  "between" (two numbers are required)                       

NO_OF_RESIDUES        If this command is used, QUEST will only search chains with    
                      number of residues in a given range.  For example, you may     
                      say that the number of residues must be ">=20".                
                      The recognised symbols are:                                    
                      <> or .NE. "not equal to"                                      
                      =  or .EQ. "equal to"                                          
                      <= or .LE. "less than or equal to"                             
                      <  or .LT. "less than"                                         
                      >= or .GE. "greater than or equal to"                          
                      >  or .GT. "greater than"                                      
                       Ð  "between" (two numbers are required)                       

FULL_CHAIN            For brevity, the default text output from PDB sequence         
                      searches shows only the portions of each chain which match     
                      the target sequence.                                           
                      The FULL_CHAIN command instructs QUEST to show the complete    
                      sequences of chains matching the target sequence.              

FULL_ALL              For brevity, the default  text output from PDB sequence        
                      searches shows only the portions of each chain which match     
                      the target sequence.                                           
                      The FULL_ALL command instructs QUEST to show the complete      
                      sequences of all chains, regardless of whether they match the  
                      target sequence.                                               

DELETE-LAST           Removes the last residue from the sequence, or from the        
                      definition if you are within PDEF.                             

DELETE-ALL            Resets either the sequence or the definitions completely.      

DEFINE-SEQUENCE       Declares that the sequence is complete, and returns to the     
                      PDB-SEARCH menu.  The QUESTÉ command may then be selected to   
                      start the search.  See also FIND-SEQUENCE below.               

FIND-SEQUENCE         Declares that the sequence is complete, and immediately        
                      starts searching for the sequence.                             



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Volume 2 Chapter 10 Search Menu *PDBSEQ.