3D-PSSM Help Page


1. Introduction

2. Submitting your query

3. Understanding your results

4. Examples

5. Citing us

6. Methods

7. Frequently Asked Questions

8. Advanced Options

9. Version History


1. Introduction

The 3D-PSSM server is a designed to take a PROTEIN sequence of interest to you, and attempt to predict its 3-dimensional structure and its probable function. We have a library of known protein structures onto each of which your sequence is "threaded" and scored for compatibility. We use a variety of scoring components: 1D-PSSMs (sequence profiles built from relatively close homologues), 3D-PSSMs (more general profiles containing more remote homologues - see Methods), matching of secondary structure elements, and propensities of the residues in your query sequence to occupy varying levels of solvent accesibility.


2. Submitting your query

If you select "Recognise a Fold" from the home page menu, you are presented with a submission form. You need to:

Your query sequence must be LESS THAN 800 RESIDUES. I am sorry for this limitation, but as the time taken for a 3D-PSSM job increases rapidly with query sequence length, this is currently necessary to allow reasonably equal use of the server by each user. As there are almost no domains in our fold library longer than 800 residues, a query sequence longer than 800 residues would EITHER not constitute a single domain that could be found in our library (hence making the search futile) OR the query sequence contains more than one domain. If you have a long query sequence, and you are not certain if it is a single domain or not, then splitting your sequence into smaller chunks (using your best guess as to the location of domain boundaries) is advised. A mechanism to automatically determine domain boundaries is currently under investigation. The format of your query sequence should adhere to one of the following:

  • Single Sequence

    >optional description
    SETVPPAPAASAAPEKPLAGKKAKKPAKAAAASKKKPAGPS
    VSELIVQAASSS
  • Pre-made 3D-PSSM Probe

    >test_seq
    >test_DSC_SS
    *
    DC 0.882
    WC 0.673
    SC 0.671
    FC 0.592
    LH 0.877
    GH 0.877
    EH 0.877
    FH 0.877
    LH 0.877
    EH 0.905
    EH 0.893
    VH 0.745
    HH 0.621
    KH 0.422
    HC 0.457
    SC 0.457
    TC 0.457
    VC 0.700
    IC 0.890
    GC 0.821
    *
    

  • CLUSTAL Multiple Sequence Alignment

    Note this is in the beta-testing phase. If you have repeated problems with submitting clustal alignments let me know (E-Mail Lawrence Kelley) Also, it should be noted that the first sequence in the clustal alignment is the one treated as the query sequence (in the case below this is sequence AAF01449).
    
    CLUSTAL W (1.8) multiple sequence alignment
    
    
    AAF01449            -----------------------------------MEVAYRFSQPHLEWNSYGHWRSSIA
    P.aeruginosa        -------------------------------------------MPSNALWLRADQLSSVS
    S25660              MRLLRFCCVLDHLICFTSPVNTFLRYNAFTLCNGEFGMSHPALTQLRALRYCK-EIPALD
    S.paratyphi         -------------------------------------MSHPALTQLRALRYFD-AIPALE
    S.enteritdis        -------------------------------------MSHPALTQLRALRYFD-AIPALE
    S.typhi             -------------------------------------MSHPALTQLRALRYFD-AIPALE
    S.typhimurium       -------------------------------------MSHPALTXXXALRYFD-AIPALE
    K.pneumoniae        -------------------------------------MSHPALTRLRALRYFA-VMPSLP
    Y.pestis            -------------------------------------MFIGDASILKPIQWCATEHPELP
    AAF41147            ---------------------------------------MEHLFGKWLPDLPAAISDGIS
    CAB84215            ---------------------------------------MEHLFEEWLPDLPADVSDGIG
    N.gonorrheae        ---------------------------------------MEHLFGKWLPDLPAPVSDGID
    S.putrefaciens      ----------------------------------MNVTSLSFPYGESIQWFCADNTKNLP
                                                                                  : 
    
    AAF01449            LAGFGRPWVYARSVISHCDVEGSDSALLQLGNIPLGSLLFGEN-------------PYKR
    P.aeruginosa        LHGHDRPWVFARSVAARSALEGSGFDLALLGTRSLGELLFSDS-------------AFER
    S25660              LCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSS-------------TLTR
    S.paratyphi         LCADGEPWLAGRTVVPESTLCGPEQVLQHLGKTPLGRYLFTSS-------------TLTR
    S.enteritdis        ------------------------------------------------------------
    S.typhi             LCADGEPWLAGRTVVPESTLCGPEQVLQHLGKTPLGRYLFTSS-------------TLTR
    S.typhimurium       LCADGEPWLAGRTVVPESTLCEPEQVLQHLGKTPLGRYLFTSS-------------TLTR
    K.pneumoniae        LNADGEPWLAGRTVARESTLCGPELALQQLGQTPLGRYLFTSS-------------TLTR
    Y.pestis            LFGDNVPWLLGRTVIPEETLSGPDRALVDLGTLPLGRYLFSGD-------------ALTR
    AAF41147            LKLDRIPVVEARSEC--RIGSAFWQNILDCGTRPLGERLFQAD------------LEGAR
    CAB84215            LKLDGIPVVAARSEC--RIGSAFWQNILDCGTRPLGERLFQAD------------LEGAR
    N.gonorrheae        LKLDGTAVVQARSAC--SVGSAFWQNILDCGTRPLGERLFQAD------------LEGAR
    S.putrefaciens      LCLDDVPWVFARTLIPQSLLSTRQADFLGLGTRPLGELLFSQDSFVPGRIEIARFATNSR
                                                                                    
    
    AAF01449            SEIEVCRYPDACNASSRPA
    P.aeruginosa        GPIEVCRYPAAGLPAEVRA
    S25660              DFIEIGRD-----------
    S.paratyphi         DFIEIGRD-----------
    S.enteritdis        -------------------
    S.typhi             DFIEIGRD-----------
    S.typhimurium       DFIEIGRD-----------
    K.pneumoniae        DFIEIGRD-----------
    Y.pestis            DYIHVGRQ-----------
    AAF41147            SAFEFAVA------GEGCG
    CAB84215            SAFEFAVF------GEGCG
    N.gonorrheae        SAFEFAVS------SEGCG
    S.putrefaciens      LAHLAQSL------AQNVE
    

    (Further help on Advanced Options )


    3. Understanding your results

    Please note there is another help file about INTERPRETING YOUR RESULTS which may be of use.