Volume 2 Chapter 10 Search Menu NUMERIC

Back to Table of Contents

PDB-SEARCH

Function

The PDB-SEARCH sub-menu is used to construct bibliographic and other simple searches of the Brookhaven Protein Data Bank (PDB) entries, all of which have been converted into the QUEST ASER search format.

When QUEST is used to search the PDB, the program will automatically start in this menu.

Only a subset of the available QUEST commands are applicable when searching the PDB. For example, there are no chemical or crystallographic structures stored in the PDB ASER file, so a connectivity search is guaranteed to produce no hits at all.

The PDB-SEARCH menu is customised to provide easy access to all the non-sequence data stored in the PDB ASER file.

Graphics QUEST3D Procedure

The PDB-SEARCH sub-menu is shown below.

This table summarises the buttons in the PDB-SEARCH sub-menu.


                     Function                                                    
Button                                                                           

PDB-ID-CODE          Prompts for a PDB ID code, for example, 1YCC, to be         
                     located in the PDB ASER database.  Each entry's PDB ID      
                     code is stored in the form: ID-1YCC in the ASER *QUALIFIER  
                     field.                                                      

*REFCODE             Prompts for a CCDC reference code (refcode) to be located  
                     in the PDB ASER database.  Each entry's PDB ID code is    
                     converted to a 6 character refcode by prefixing the PDB ID  
                     code with a zero, suffixing it with a zero, and moving the  
                     PDB numerical prefix to the end of the refcode.  For     
                     example, 1YCC becomes 0YCC01.  This is done so that     
                     related PDB entries (1YCC,  2YCC, etc.) will be grouped   
                     together when the ASER file is sorted into alphanumeric   
                     order by refcode.                      
                      

SEQUENCE-SEARCH...   Enters the PDB-SEQUENCE search menu, which is described in  
                     the new manual pages 10-27aÉ                                

COMPND               Prompts for some text to be located in the PDB COMPND       
                     field.                                                      
                                                                                 
                     For example, the PDB line:                                  
                     COMPND    CYTOCHROME C (ISOZYME 1) (REDUCED)                
                     will be stored as follows in the database as:               
                     Cytochrome c (isozyme 1) (reduced)                          

SOURCE               Prompts for some text to be located in the PDB SOURCE       
                     field.                                                      
                                                                                 
                     For example, the PDB line:                                  
                     SOURCE    BAKER'S YEAST (SACCHAROMYCES $CEREVISIAE)         
                     will be stored as follows in the database as:               
                     Source: Baker's yeast (Saccharomyces cerevisiae)            

CLASSIFICATION       Prompts for some text to be located in the PDB functional   
                     classification field.                                       
                                                                                 
                     For example, the PDB line:                                  
                     HEADER    ELECTRON TRANSPORT (CYTOCHROME)                   
                     will be stored as follows in the database as:               
                     Class:Electron transport (cytochrome)                       

CONTRIBUTOR          Prompts for some text to be located in the PDB data         
                     contributors field.                                         
                                                                                 
                     For example, the PDB line:                                  
                     AUTHOR    G.V.LOUIE,G.D.BRAYER                              
                     will be stored as follows in the database as:               
                     Data contributed by G.V.Louie,G.D.Brayer                    

DEPOSITION-DATE      Prompts for some text to be located in the PDB deposition   
                     date field.  This is stored as text in the ISO format (2    
                     digits for year, 2 digits for month, 2 digits for date),    
                     and so searches on ranges of dates are not possible.        
                                                                                 
                     For example, the date in the PDB line:                      
                                                                                 
                     HEADER    ELECTRON TRANSPORT (CYTOCHROME)                   
                     09-MAY-90   1YCC      1YCC   2                              
                     will be stored as follows in the database as:               
                     Deposition date 900509                                      

*JRNL                Each of these buttons prompts for information to be         
*CODEN               located from the PDB JRNL field.                            
*VOLUME                                                                          
*YEAR                For example, the PDB field:                                 
*AUTHOR              JRNL AUTH   G.V.LOUIE,G.D.BRAYER                            
                     JRNL TITL   HIGH-RESOLUTION REFINEMENT OF YEAST             
                     JRNL TITL 2 ISO-1-*CYTOCHROME $C AND COMPARISONS WITH       
                     OTHER                                                       
                     JRNL TITL 3 EUKARYOTIC CYTOCHROMES $C                       
                     JRNL REF    J.MOL.BIOL.                   V. 214   527      
                     1990                                                        
                     JRNL REFN   ASTM JMOBAK  UK ISSN 0022-2836                  
                      070                                                        
                                                                                 
                     will be stored as follows in the database as:               
                     *JRNL = J.Mol.Biol.,                                        
                     *CODEN = 70                                                 
                     *VOLUME = 214                                               
                     *PAGE = 527                                                 
                     *YEAR = 1990                                                
                     *AUTH = G.V.Louie,G.D.Brayer                                
                                                                                 

*SURNAME             Prompts for a complete surname to be located in the PDB     
                     JRNL/AUTH field (as opposed to *AUTHOR which searches for   
                     substrings of this PDB field).  *SURNAME is particularly    
                     useful when searching for very short names.                 

RESOLUTION           Prompts for a resolution (in ngstroms) to be located.      
                     Note that since the resolution is stored as text in the     
                     database, it is not possible to search for ranges of        
                     values.                                                     
                                                                                 
                     For example, the PDB line:                                  
                     REMARK   2 RESOLUTION. 1.23 ANGSTROMS.                      
                     will be stored as follows in the ASER *QUALIFER field:      
                     Resolution 1.23A                                            

NMR                  There is no prompt for this command.  It immediately        
                     creates a QUEST *QUALIFIER test, searching for the text     
                     "Experimental:NMR".                                         
                                                                                 
                     For example, the PDB line:                                  
                     EXPDTA    NMR                                               
                     will be stored as follows in the database as:               
                     Experimental:NMR                                            

THEORETICAL-MODEL    There is no prompt for this command.  It immediately        
                     creates a QUEST *QUALIFIER test, searching for the text     
                     "Experimental:theoretical model".                           
                                                                                 
                     For example, the PDB line:                                  
                     EXPDTA    THEORETICAL MODEL                                 
                     will be stored as follows in the database as:               
                                                                                 
                     Experimental:theoretical model                              

MAXIMUM-HITS         Prompts for the maximum number of "hit" entries allowable   
                     during this QUEST search.                                   

BEGIN-AT-REFCODE     Prompts for a refcode from which subsequent QUEST searches  
                     will start.  Note that the given refcode does not have to   
                     exist in the database; the next entry in alphabetical       
                     order after the given refcode will be used.                 

HITALL&START         Declares that every entry in the PDB database should be a   
                     "hit", and starts "browsing" immediately.                   

FASTQUEST            For a description of this command, see Section 10, Page     
                     13, Volume 2 of the Cambridge Structural Database System    
                     documentation.                                              

QUEST...             For a description of this command, see Section 10, Page     
                     46, Volume 2 of the Cambridge Structural Database System    
                     documentation.                                              



Back to Table of Contents

Volume 2 Chapter 10 Search Menu PDB-SEQUENCE.