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AntiJen    a kinetic, thermodynamic and cellular database v2.0 

THE ANTIJEN DATABASE QUERY GUIDE
     The AntiJen Database Query Guide aims to help the user conduct more effective database searches.

The search criteria required to make a detailed search or a broad search are entered into a single category-specific search page. The title and identity of each search field are outlined here and examples of valid field values given.
 
MHC LIGAND SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

ASPFPFDL

**SPFPF*L

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers. Minimum epitope amino acid length: 6. Maximum epitope amino acid length: 29.

Epitope length of 10 only required: MIN: 10 MAX: 10.

Epitope length of 9, 10, 11 or 12 required: MIN: 9 MAX: 12

Epitope length of 12 or less required: MAX 12 (N.B. No MIN value)

3  ALLELE or SEROTYPE Non-mandatory. To narrow a search select the required ALLELE or SEROTYPE from the alphabetically ordered dropdown menu. If the desired option is missing then it is likely it does not exist in the database.

A*0202

 

DR12

4  DATA
IC50(R) Non-mandatory. Ameasure of the effectiveness of binding. (nM) 700
IC50(F) Non-mandatory. Effectiveness of binding measured in fluorescence. (nM) 110
BL50 Non-mandatory. (nM) 49375
ka Non-mandatory. (M-1) 1500000
kd Non-mandatory. Dissociation constant (M) 0.0012
Tm Non-mandatory. Stable temperature (C) 25
    

 

     
    

 

MHC LIGAND KINETIC DATA SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

IAYLKQAT

***IAYLKQAT*

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers.Minimum epitope amino acid length: 7. Maximum epitope amino acid length: 25.

Epitope length of 16 only required: MIN: 16 MAX: 16.

Epitope length of between 9 and 16 required: MIN: 9 MAX: 16

3  ALLELE or SEROTYPE Non-mandatory. To narrow a search select the required ALLELE or SEROTYPE from the alphabetically ordered dropdown menu. If the desired option is missing then it is likely it does not exist in the database.

I-Ek

4  DATA
k1 Non-mandatory. (M-1 s-1) 40000
k-1 Non-mandatory. (s-1) 0.000078
t1/2 (kinetics) Non-mandatory. (hour) 17.5
t1/2 (B2M) Non-mandatory. (hour) 16.2
t1/2 (cell surface) Non-mandatory. (hour) 2.5
    

 

     
    

 

T CELL EPITOPE SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

LFAAFPSFA

TT*A**VNI

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers. Minimum epitope amino acid length: 7. Maximum epitope amino acid length: 38.

Epitope length of 8 only required: MIN: 8 MAX: 8.

Epitope length between 30 and 32 required: MIN: 30 MAX: 32

Epitope length of 12 or less required: MAX 12 (N.B. No MIN value)

3  ALLELE or SEROTYPE Non-mandatory. To narrow a search select the required ALLELE or SEROTYPE from the alphabetically ordered dropdown menu. If the desired option is missing then it is likely it does not exist in the database.

A*0201

 

I-Ab

    

 

     
    

 

TCR-MHC COMPLEX DATA SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

ANERADLIAYLKQATK

RY*PG**AL

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers.Minimum epitope amino acid length: 5. Maximum epitope amino acid length: 24.

Epitope length of 24 only required: MIN: 24 MAX: 24.

Epitope length between 8 and 12 required: MIN: 8 MAX: 12

Epitope length of 10 or less required: MAX 10 (N.B. No MIN value)

3  ALLELE or SEROTYPE Non-mandatory. To narrow a search select the required ALLELE or SEROTYPE from the alphabetically ordered dropdown menu. If the desired option is missing then it is likely it does not exist in the database.

I-Ek

 

Cw*0702

4  DATA
kd Non-mandatory. (nM) 320000
EC50 Non-mandatory. (nM) 2000
k1 Non-mandatory. (M-1 s-1) 3200
k-1 Non-mandatory. (s-1). 0.049
ka Non-mandatory. (M-1) 2000000
t1/2 Non-mandatory. (min). 0.146
    

 

     
    

 

TAP LIGAND SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

APDAPDEFSAAAAY

AAA*AAAAY

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers. Minimum epitope amino acid length: 7. Maximum epitope amino acid length: 17.

Epitope length of 10 only required: MIN: 10 MAX: 10.

Epitope length of 9, 10, 11 or 12 required: MIN: 9 MAX: 12

Epitope length of 12 or less required: MAX 12 (N.B. No MIN value)

3  DATA
IC50 (R) Non-mandatory. (nM) 11000
KD Non-mandatory. (nM) 4300
    

 

     
    

 

B CELL EPITOPE SEARCH
    Minimum search requirement : A minimum of three amino acids must be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  EPITOPE STRING Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk.

CFDDTDPIKK

SS*DN*K*F

2  LENGTH OF AMINO ACID STRING Non-mandatory. Either both, one or neither of the amino acid length minimum and maximum size windows can be used. Numbers entered should be whole numbers. Minimum epitope amino acid length: 4. Maximum epitope amino acid length: 38.

Epitope length of 38 only required: MIN: 38 MAX: 38.

Epitope length of between 8 and 12 required: MIN: 8 MAX: 12

Epitope length of 12 or less required: MAX 12 (N.B. No MIN value)

    

 

     
    

 

IMMUNOLOGICAL PROTEIN-PROTEIN INTERACTION SEARCH
    Minimum search requirement : Default values.
FIELD DESCRIPTION
1  MOLECULE A Identical molecule drop down to molecule B excluding the 'any molecule' option. The default here is set to 'MHC'.
2  MOLECULE B Identical molecule drop down to molecule A, however includes an 'any molecule' option which is set to default.
    

 

     
    

 

KEYWORD SEARCH
    Minimum search requirement : An entry of two letters minimum is required. Search is case insensitive.
FIELD DESCRIPTION
KEYWORDS

Keywords entered are considered case insensitive.Up to 250 characters (including spaces) can be entered.

To search for several keywords at one time, delimit keywords or phrases to be considered using a semicolon(;).

To consider keywords together, use words 'AND' & 'OR'.

EXAMPLES: Words and Phrases

Bacteria    Results returned will match the word, 'Bacteria'.

Hepatitis B     Results returned will match the phrase, 'Hepatitis B'.

mycobacterium tuberculosis     Results returned will match the phrase, 'mycobacterium tuberculosis'.

proteins of the antigen 85 complex      Results returned will match this complete string.

 

EXAMPLES: Delimited words and phrases

hiv; bowel; cancer      Results returned will match any of keywords used.

mycobacterium; tuberculosis      Results returned will match either keyword used.

proteins; antigen 85 complex      Results returned will match either the keyword ('proteins') or                                                             complete phrase ('antigen 85 complex')

EXAMPLES: Using AND / OR clauses

hiv AND bowel      Results returned where both keywords are matched.

HIV OR human immunodeficiency virus      Results returned where either the keyword ('HIV') or                                                                         the complete phrase ('human immunodeficiency virus') is                                                                         matched.

Other valid searches:

  • hiv AND bowel; bacteria
  • bacteria AND protein; hiv OR bowel
  • bacteria AND protein AND antigen 85
Invalid searches

  • bacteria AND protein OR antigen 85
  • hiv bowel bacteria
   
   
   
DIFFUSION COEFFICIENT SEARCH
    Minimum search requirement : No minimum requirement
FIELD DESCRIPTION EXAMPLE
1  PROTEIN DIFFUSING TYPE Non-Mandatory. Select a type from the available pull-down. Con A receptor
2  DATA
DIFFUSION COEFFICIENT Non-mandatory. (e-10 cm2 s-1) 0.36
FRICTION COEFFICIENT Non-mandatory. (pN/(um/s)) 0.25
   
   
   
PEPTIDE LIBRARIES SEARCH
    Minimum search requirement : Either a name OR an allele or sub-type should be selected from the appropriate pull down menus.
FIELD DESCRIPTION EXAMPLE
1  NAME Non-Mandatory. Select a type from the available pull-down. UDAKA00
2  ALLELE or SEROTYPE Non-Mandatory. Select a type from the available pull-down. H-2Kb
3  LIMITING AMINO ACID Non-Mandatory. Select a single-letter amino acid code from the available pull-down G
    AMINO ACID POSITION Non-Mandatory. Select a position number from the available pull-down 1
4  DATA
RELATIVE IC50 Non-mandatory. 0.57
LOG RELATIVE SC50 Non-mandatory. 0.69
LOG SI Non-mandatory. 0.177
   
   
   
COPY NUMBERS SEARCH
    Minimum search requirement : Either a cell type OR a protein description should be selected from the appropriate pull down menus, OR a minimum of three amino acids should be nominated. These amino acids can be within a sequential string or contain intermittent variable amino acid positions, indicated using asterisks (*). Alternative amino acids should be encased in square brackets ([]).
FIELD DESCRIPTION EXAMPLE
1  CELL TYPE Non-Mandatory. Select a type from the available pull-down. B-lymphocytes
2  PROTEIN DESCRIPTION Non-Mandatory. Select a description from the available pull-down. monoclonal antibody
3  EPITOPE STRING Non-Mandatory. A minimum requirement of 3 amino acids should be entered, in sequential order. Variable amino acid positions are replaced with an asterisk. DTQF
4  DATA
NUMBER OF MOLECULES PER CELL Non-mandatory. 342000
NUMBER OF COMPLEXES Non-mandatory. 32820
ABUNDANCY Non-mandatory. (e-7) 23
   
   
   
VARIABLE AMINO ACID SEARCH FUNCTIONALITY
   

When submitting an epitope string on a search form, some amino acid positions may be replaced with an asterisk (*). This position will be tagged as a 'variable position', and can be substituted with any amino acid to match the requested string. A minimum of 3 single-letter amino acid codes are required. The number of asterisks included is unlimited.

For example, a MHC Ligand search for epitope AE*YAAAAAA*AAAA , will return four matching epitopes: AEAYAAAAAAKAAAA; AEEYAAAAAAKAAAA; AEKYAAAAAAAAAAA and AEKYAAAAAAKAAAA.

This fuctionality is available on all search forms with accepts 'epitope string' as a search criteria. i.e. MHC Ligand,  MHC Kinetics,   T Cell Epitope,   TCR-MHC,   TAP Ligand,   B Cell Epitope   &   Copy Numbers   search forms.

   
   
   
ALTERNATIVE AMINO ACID SEARCH FUNCTIONALITY
   

When submitting an epitope string on a search form, some amino acid positions may be required to be occupied by specific alternative residues. The number of alternative amino acids within one set should be at least two residues and limited to five residues, with four alternative sets per epitope string.The required alternatives should be included in square brackets.

For example an MHC Ligand search for epitope AE[AEK]YAAAAAA[KA]AAAA, will return five matching epitopes: AEAYAAAAAAKAAAA; AEEYAAAAAAKAAAA; AEKYAAAAAAAAAAA , AEKYAAAAAAKAAAA and AKKAAEAYAAAAAAA.

This fuctionality is available on all search forms with accepts 'epitope string' as a search criteria. i.e. MHC Ligand,  MHC Kinetics,   T Cell Epitope,   TCR-MHC,   TAP Ligand,   B Cell Epitope   &   Copy Numbers   search forms.

   
   
   
USING DATA RADIOBUTTONS
   

Data radiobuttons are available to serve as data filters. They allow the user to target desirable information and discard unwanted figures. This delivers a more ordered results page and improves response time.

By default, no radiobuttons are selected and all data matching the rest of the search criteria is returned. However, when a radiobutton is selected it will return information stored for that data-type only.

For example, you wish to do an MHC Ligand search for epitope string 'GIGI', but you only require results which have IC50 data associated with them. An epitope search without the IC50 radiobutton selected returns 22 results, some are useful some not. A search using the IC50 radiobutton filter returns 10 valid results.

Radiobutton data filters are found on the following search pages: MHC Ligand,  MHC Kinetics,  TCR-MHC,   TAP Ligand,    Diffusion Coefficient,  Peptide Libraries,  &   Copy Numbers.

   
   
 
 
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