## SIGGENLIG documentation

## CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

## 1.0 SUMMARY

Generates ligand-binding signatures from a CON file (contacts file) of residue-ligand contacts. Generates ligand-binding signatures from a CON file

## 2.0 INPUTS & OUTPUTS

SIGGENLIG reads a CON file of residue-ligand contacts generated by using SITES and a directory of CCF files (clean coordinate files) containing a CCF file for each protein or domain in the CON file. One or more signature files, each containing a ligand-binding signature, are generated for each ligand-binding site in the CON file. The user specifies whether 1D (sequence) or 3D (structural) signatures are generated and whether they are 'full-length' (signature corresponds to entire ligand-binding site) or 'patch' (signature corresponds to part of ligand-binding site). For 3D signatures, the environment definition is specified and for patch signatures, a 'Minimum patch size' and 'Maximum gap distance' are specified. A 'Window size' is specified for all signatures. The paths of the CCF files (input) and signature files (output) are specified by the user and the file extensions are specified in the ACD file. A log file is also written.

## 3.0 INPUT FILE FORMAT

The format of the CON file (contacts file) is described in SITES documentation. The format of the CCF files is described in PDBPARSE documentation (proteins) and the DOMAINER documentation (domains).

### Input files for usage example

### File: ../sites-keep/SITES.con

    XX   Residue-ligand contact data (for domains).
    XX
    TY   LIGAND
    XX
    EX   THRESH 1.0; IGNORE .; NMOD .; NCHA .;
    XX
    NE   11
    XX
    EN   [1]
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG 101;
    XX
    DE   2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
    XX
    SI   SN 1; NS 2
    XX
    CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .
    XX
    S1   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
         ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
    XX
    NC   SM .; LI 6
    XX
    LI   ASP 2
    LI   PHE 6
    LI   THR 7
    LI   LEU 44
    LI   GLY 45
    LI   ASP 46
    XX
    //
    EN   [2]
    XX
    ID   PDB 1ii7; DOM d1ii7a_; LIG 101;
    XX
    DE   2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
    XX
    SI   SN 2; NS 2
    XX
    CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 .
    XX
    S1   SEQUENCE    65 AA;   7395 MW;  75FBE75B22FD3678 CRC64;
         MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
         LKKAI
    XX
    NC   SM .; LI 2
    XX
    LI   HIS 10
    LI   ASP 49
    XX

      [Part of this file has been deleted for brevity]

    NC   SM .; LI 3
    XX
    LI   ASP 8
    LI   HIS 10
    LI   ASP 49
    XX
    //
    EN   [10]
    XX
    ID   PDB 2hhb; DOM .; LIG PO4;
    XX
    DE   PHOSPHATE ION
    XX
    SI   SN 1; NS 1
    XX
    CN   MO .; CN1 1; CN2 .; ID1 D; ID2 .; NRES1 146; NRES2 .
    XX
    S1   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
         VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
         KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
         EFTPPVQAAY QKVVAGVANA LAHKYH
    XX
    NC   SM .; LI 2
    XX
    LI   VAL 1
    LI   LEU 81
    XX
    //
    EN   [11]
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG POP;
    XX
    DE   PYROPHOSPHATE 2-
    XX
    SI   SN 1; NS 1
    XX
    CN   MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 .
    XX
    S1   SEQUENCE    52 AA;   5817 MW;  D8CCAE0E1FC0849A CRC64;
         ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
    XX
    NC   SM .; LI 6
    XX
    LI   ASP 2
    LI   ILE 3
    LI   GLU 4
    LI   GLY 5
    LI   PHE 6
    LI   THR 7
    XX
    //

## 4.0 OUTPUT FILE FORMAT

The output file (Figure 1) uses the standard signature file format and is described in the SIGGEN documentation. For the ligand-binding signatures generated by SIGGENLIG, however, four additional lines of bibliographic information taken from the CON (input) file are written to a signature file. The records have the following meaning:

- ID - identifier codes: (1) PDB: 4-character PDB identifier code. (2) DOM: 7-character domain identifier code from SCOP or CATH. (3) LIG: Ligand identifier (an abbreviation of its full name).
- DE - full name of the ligand, see HETPARSE documentation.
- IS - ligand-binding site information: (1) SN: Site number. This uniquely identifies a ligand-binding site in the CON file generated by running SITES. (2) NS: The total number of binding sites for a given ligand.
- IP - path information: (1) PN: Patch number. The sequential order (from the N-terminus) of the patch in the ligand-binding site. (2) NP: Number of patches. The total number of patches in this ligand-binding site. (3) MP: Minimum patch size. (4) MG: Maximum gap distance. MP and MG were specified in the generation of the signature (see 'Algorithm' below).

In addition, where 3D signatures are generated, the following records have different meanings than for 1D signatures (e.g. those generated by using SIGGEN):

- IN - Informative line about signature position. The number of different observed amino acid environments (rather than residue identities) is given after 'NRES'
- AA - The identifier of an environment (rather than residue) seen in this position and the frequency of its occurence are delimited by ';'.

### Output files for usage example

### File: 101.1.F.#.1cs4.d1cs4a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG 101;
    XX
    DE    2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
    XX
    IS   SN 1; NS 2
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   6
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   1 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   3 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   T ; 1
    XX
    GA   0 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   36 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   G ; 1
    XX
    GA   0 ; 1
    XX
    NN   [6]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   0 ; 1
    //

### File: 101.2.F.#.1ii7.d1ii7a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1ii7; DOM d1ii7a_; LIG 101;
    XX
    DE    2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE
    XX
    IS   SN 2; NS 2
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   2
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   H ; 1
    XX
    GA   9 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   38 ; 1
    //

### File: FOK.1.F.#.1cs4.d1cs4a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG FOK;
    XX
    DE    FORSKOLIN
    XX
    IS   SN 1; NS 1
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   1
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   43 ; 1
    //

### File: HEM.1.F.#.2hhb...sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 2hhb; DOM .; LIG HEM;
    XX
    DE    PROTOPORPHYRIN IX CONTAINING FE
    XX
    IS   SN 1; NS 4
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   17
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   Y ; 1
    XX
    GA   41 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   H ; 1
    XX
    GA   1 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX

      [Part of this file has been deleted for brevity]

    XX
    GA   0 ; 1
    XX
    NN   [12]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   3 ; 1
    XX
    NN   [13]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   V ; 1
    XX
    GA   1 ; 1
    XX
    NN   [14]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   N ; 1
    XX
    GA   3 ; 1
    XX
    NN   [15]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [16]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   2 ; 1
    XX
    NN   [17]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   34 ; 1
    //

### File: HEM.2.F.#.2hhb...sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 2hhb; DOM .; LIG HEM;
    XX
    DE    PROTOPORPHYRIN IX CONTAINING FE
    XX
    IS   SN 2; NS 4
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   17
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   30 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   9 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   H ; 1
    XX
    GA   20 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX

      [Part of this file has been deleted for brevity]

    XX
    GA   0 ; 1
    XX
    NN   [12]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   3 ; 1
    XX
    NN   [13]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   V ; 1
    XX
    GA   1 ; 1
    XX
    NN   [14]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   N ; 1
    XX
    GA   3 ; 1
    XX
    NN   [15]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [16]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   2 ; 1
    XX
    NN   [17]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   34 ; 1
    //

### File: HEM.3.F.#.2hhb...sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 2hhb; DOM .; LIG HEM;
    XX
    DE    PROTOPORPHYRIN IX CONTAINING FE
    XX
    IS   SN 3; NS 4
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   19
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   M ; 1
    XX
    GA   31 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   T ; 1
    XX
    GA   6 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   Y ; 1
    XX
    GA   2 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX

      [Part of this file has been deleted for brevity]

    XX
    GA   0 ; 1
    XX
    NN   [14]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   3 ; 1
    XX
    NN   [15]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   V ; 1
    XX
    GA   1 ; 1
    XX
    NN   [16]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   N ; 1
    XX
    GA   3 ; 1
    XX
    NN   [17]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [18]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   2 ; 1
    XX
    NN   [19]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   34 ; 1
    //

### File: HEM.4.F.#.2hhb...sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 2hhb; DOM .; LIG HEM;
    XX
    DE    PROTOPORPHYRIN IX CONTAINING FE
    XX
    IS   SN 4; NS 4
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   15
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   30 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   9 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   H ; 1
    XX
    GA   20 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX

      [Part of this file has been deleted for brevity]

    XX
    GA   0 ; 1
    XX
    NN   [10]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   3 ; 1
    XX
    NN   [11]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   V ; 1
    XX
    GA   1 ; 1
    XX
    NN   [12]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   N ; 1
    XX
    GA   3 ; 1
    XX
    NN   [13]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [14]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   2 ; 1
    XX
    NN   [15]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   34 ; 1
    //

### File: MG.1.F.#.1cs4.d1cs4a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG MG;
    XX
    DE    MAGNESIUM ION
    XX
    IS   SN 1; NS 1
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   4
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   1 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   I ; 1
    XX
    GA   0 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   2 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   39 ; 1
    //

### File: MN.1.F.#.1ii7.d1ii7a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1ii7; DOM d1ii7a_; LIG MN;
    XX
    DE    MANGANESE (II) ION
    XX
    IS   SN 1; NS 1
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   3
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   7 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   H ; 1
    XX
    GA   1 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   38 ; 1
    //

### File: PO4.1.F.#.2hhb...sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 2hhb; DOM .; LIG PO4;
    XX
    DE    PHOSPHATE ION
    XX
    IS   SN 1; NS 1
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   2
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   V ; 1
    XX
    GA   0 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   L ; 1
    XX
    GA   79 ; 1
    //

### File: POP.1.F.#.1cs4.d1cs4a_.sig

    TY   LIGAND
    XX
    TS   1D
    XX
    ID   PDB 1cs4; DOM d1cs4a_; LIG POP;
    XX
    DE    PYROPHOSPHATE 2-
    XX
    IS   SN 1; NS 1
    XX
    IP   PN 0; NP 0; MP 5; MG 2
    XX
    NP   6
    XX
    NN   [1]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   D ; 1
    XX
    GA   1 ; 1
    XX
    NN   [2]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   I ; 1
    XX
    GA   0 ; 1
    XX
    NN   [3]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   E ; 1
    XX
    GA   0 ; 1
    XX
    NN   [4]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   G ; 1
    XX
    GA   0 ; 1
    XX
    NN   [5]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   F ; 1
    XX
    GA   0 ; 1
    XX
    NN   [6]
    XX
    IN   NRES 1 ; NGAP 1 ; WSIZ 0
    XX
    AA   T ; 1
    XX
    GA   0 ; 1
    //

### File: siggenlig.log

## 5.0 DATA FILES

SIGGENLIG does not use any data files.

## 6.0 USAGE

    Generates ligand-binding signatures from a CON file
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-confile]           infile     This option specifies the name of the CON
                                      file (contact file) (input). A 'contact
                                      file' contains contact data for a protein or
                                      a domain from SCOP or CATH, in the CON
                                      format (EMBL-like). The contacts may be
                                      intra-chain residue-residue, inter-chain
                                      residue-residue or residue-ligand. The files
                                      are generated by using CONTACTS, INTERFACE
                                      and SITES.
       -ccfpdir            directory  This option specifies the location of
                                      protein CCF file (clean coordinate files)
                                      (input). A 'clean cordinate file' contains
                                      protein coordinate and derived data for a
                                      single PDB file ('protein clean coordinate
                                      file') or a single domain from SCOP or CATH
                                      ('domain clean coordinate file'), in CCF
                                      format (EMBL-like). The files, generated by
                                      using PDBPARSE (PDB files) or DOMAINER
                                      (domains), contain 'cleaned-up' data that is
                                      self-consistent and error-corrected.
                                      Records for residue solvent accessibility
                                      and secondary structure are added to the
                                      file by using PDBPLUS. default: ./
       -ccfddir            directory  This option specifies the location of
                                      protein CCF file (clean coordinate files)
                                      (input). A 'clean cordinate file' contains
                                      protein coordinate and derived data for a
                                      single PDB file ('protein clean coordinate
                                      file') or a single domain from SCOP or CATH
                                      ('domain clean coordinate file'), in CCF
                                      format (EMBL-like). The files, generated by
                                      using PDBPARSE (PDB files) or DOMAINER
                                      (domains), contain 'cleaned-up' data that is
                                      self-consistent and error-corrected.
                                      Records for residue solvent accessibility
                                      and secondary structure are added to the
                                      file by using PDBPLUS. default: ./
       -mode               menu       [1] This option specifies the mode of
                                      signature generation. In 'Full-length
                                      signature mode' (mode 1) a single signature
                                      incorporating all residue positions that
                                      contact the ligand plus intervening gaps is
                                      generated. In 'Patch signature mode' (mode
                                      2) one or more signatures corresponding to
                                      'patches' of residue positions are
                                      generated. A patch is a set of residues that
                                      are near-neighbours in sequence and is
                                      described by two user-defined parameters:
                                      minimum patch size and maximum gap distance.
                                      (Values: 1 (Full-length signature mode); 2
                                      (Patch signature mode))
       -type               menu       [1] This option specifies the type of
                                      signature generated. In '1D (sequence)
                                      signature' sequence-based signatures are
                                      generated. In '3D (structural) signature'
                                      structure-based signatures are generated.
                                      (Values: 1 (1D (sequence) signature); 2 (3D
                                      (structural) signature))
    *  -patchsize          integer    [5] This option specifies the minimum patch
                                      size. This is the minimum number of contact
                                      positions that must be incorporated in a
                                      signature. (Integer 3 or more)
    *  -gapdistance        integer    [2] This option specifies the maximum gap
                                      distance. This is the maximum allowable gap
                                      (residues) between two residue in a patch.
                                      If two contact residues are further than
                                      this distance apart in sequence, they would
                                      not belong to the same patch. (Integer 0 or
                                      more)
    *  -environment        menu       [1] This option specifies the environment
                                      definition. See matgen3d documentation for
                                      description of definitions. (Values: 1
                                      (Env1); 2 (Env2); 3 (Env3); 4 (Env4); 5
                                      (Env5); 6 (Env6); 7 (Env7); 8 (Env8); 9
                                      (Env9); 10 (Env10); 11 (Env11); 12 (Env12);
                                      13 (Env13); 14 (Env14); 15 (Env15); 16
                                      (Env16))
       -wsiz               integer    [0] This option specifies the window size.
                                      When a signature is aligned to a protein
                                      sequence, the permissible gaps between two
                                      signature positions is determined by the
                                      empirical gaps and the window size. The user
                                      is prompted for a window size that is used
                                      for every position in the signature. Likely
                                      this is not optimal. A future implementation
                                      will provide a range of methods for
                                      generating values of window size depending
                                      upon the alignment (window size is
                                      identified by the WSIZ record in the
                                      signature output file). (Any integer value)
      [-sigoutdir]         outdir     [./] This option specifies the location of
                                      signature files (output). A 'signature file'
                                      contains a sparse sequence signature
                                      suitable for use with the SIGSCAN and
                                      SIGSCANLIG programs. The files are generated
                                      by using SIGGEN and SIGGENLIG.
      [-logfile]           outfile    [siggenlig.log] Domainatrix log output file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-logfile" associated qualifiers
       -odirectory3        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

### 6.1 COMMAND-LINE ARGUMENTS

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers

[-confile]
(Parameter 1)

infile

This option specifies the name of the CON file (contact file) (input). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES.

Input file

Required

-ccfpdir

directory

This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./

Directory

-ccfddir

directory

This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./

Directory

-mode

list

This option specifies the mode of signature generation. In 'Full-length signature mode' (mode 1) a single signature incorporating all residue positions that contact the ligand plus intervening gaps is generated. In 'Patch signature mode' (mode 2) one or more signatures corresponding to 'patches' of residue positions are generated. A patch is a set of residues that are near-neighbours in sequence and is described by two user-defined parameters: minimum patch size and maximum gap distance.

1 | (Full-length signature mode)
2 | (Patch signature mode)

1

-type

list

This option specifies the type of signature generated. In '1D (sequence) signature' sequence-based signatures are generated. In '3D (structural) signature' structure-based signatures are generated.

1 | (1D (sequence) signature)
2 | (3D (structural) signature)

1

-patchsize | integer | This option specifies the minimum patch size. This is the minimum number of contact positions that must be incorporated in a signature. | Integer 3 or more | 5
-gapdistance | integer | This option specifies the maximum gap distance. This is the maximum allowable gap (residues) between two residue in a patch. If two contact residues are further than this distance apart in sequence, they would not belong to the same patch. | Integer 0 or more | 2

-environment

list

This option specifies the environment definition. See matgen3d documentation for description of definitions.

1 | (Env1)
2 | (Env2)
3 | (Env3)
4 | (Env4)
5 | (Env5)
6 | (Env6)
7 | (Env7)
8 | (Env8)
9 | (Env9)
10 | (Env10)
11 | (Env11)
12 | (Env12)
13 | (Env13)
14 | (Env14)
15 | (Env15)
16 | (Env16)

1

-wsiz

integer

This option specifies the window size. When a signature is aligned to a protein sequence, the permissible gaps between two signature positions is determined by the empirical gaps and the window size. The user is prompted for a window size that is used for every position in the signature. Likely this is not optimal. A future implementation will provide a range of methods for generating values of window size depending upon the alignment (window size is identified by the WSIZ record in the signature output file).

Any integer value

0

[-sigoutdir] (Parameter 2) | outdir | This option specifies the location of signature files (output). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN and SIGSCANLIG programs. The files are generated by using SIGGEN and SIGGENLIG. | Output directory | ./
[-logfile] (Parameter 3) | outfile | Domainatrix log output file | Output file | siggenlig.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-logfile" associated outfile qualifiers
-odirectory3 -odirectory_logfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

### 6.2 EXAMPLE SESSION

An example of interactive use of SIGGENLIG is shown below. Here is a sample session with siggenlig

    % siggenlig
    Generates ligand-binding signatures from a CON file
    Structure contacts file: ../sites-keep/SITES.con
    Clean protein structure coordinates directory (optional) [.]: ../pdbplus-keep
    Clean domain coordinates directory (optional) [.]: ../domainer-keep
    Available modes
             1 : Full-length signature mode
             2 : Patch signature mode
    Select mode of operation. [1]: 1
    Available types
             1 : 1D (sequence) signature
             2 : 3D (structural) signature
    Select type of signature. [1]: 1
    Window size [0]:
    Domainatrix signature file output directory [./]:
    Domainatrix log output file [siggenlig.log]:

Go to the input files for this example
Go to the output files for this example

## 7.0 KNOWN BUGS & WARNINGS

Window size
The user is prompted for a window size that is used for every position in the signature. Likely this is not optimal. A future implementation will provide a range of methods for generating values of window size depending upon the alignment (window size is identified by the WSIZ record in the signature output file).

## 8.0 NOTES

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
Contact file (residue-ligand contacts) | CON format (EMBL-like.) | Residue-ligand contact data for a protein or a domain from SCOP or CATH. | SITES | N.A.
Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCAN program. Contains a sparse sequence signature. | SIGGEN, LIBGEN | The files are generated by using SIGGENLIG.

## 9.0 DESCRIPTION

A protein or a single domain of a protein may contain one or more ligand-binding sites. SIGGENLIG provides an automated means to generate signatures of ligand-binding from a CON file (contacts file) of residue-ligand contacts. The signatures generated may be of two types, 1D or 3D. 1D signatures represent protein sites as residue identitites whereas 3D signatures represent sites as residue environments in space.

## 10.0 ALGORITHM

The user specifies whether 1D (sequence) or 3D (structural) signatures are generated and whether they are 'full-length' (signature corresponds to entire ligand-binding site) or 'patch' (signature corresponds to part of ligand-binding site). For 3D signatures, the environment definition is specified and for patch signatures, a 'Minimum patch size' and 'Maximum gap distance' are specified. A 'Window size' is specified for all signatures.
Definition of full-length and patch signatures
For each ligand-binding site represented in the CON file (input), one or more signatures are generated as follows: (1) a single 'full-length' signature incorporating all residue positions that contact the ligand plus intervening gaps, or (2) one or more signatures corresponding to 'patches' of residue positions.
A patch is a set of residues that are near-neighbours in sequence and is described by two user-defined parameters as follows. (1) Minimum patch size; the minimum number of contact positions that must be incorporated for a patch to be defined. (2) Maximum gap distance. The maximum allowable gap (residues) between two residue in a patch. If two contact residues are further than this distance apart in sequence, they would not belong to the same patch.
Environment definitions.
See MATGEN3d documentation for environment definitions.
Naming of output files. The naming convention of the signature (output) files is as follows:
Ligand identifier.Site number.F or P.Patch number-Total patches.PDB identifier.Domain identifier.

- The ligand identifier is a 3-letter code that uniquely identifies the ligand.
- The site number uniquely identifies a ligand-binding site in the CON file generated by running SITES.
- F signifies a 'Full-length' and P a 'Patch' signature.
- Patch number is the sequential order (from the N-terminus) of the patch in the ligand-binding site.
- Total patches is the total number of patches for this ligand-binding site. The patch number and total number of patches are only specified for a 'patch'.
- PDB identifier code.
- Domain identifier code. Only specified if the binding site is mapped to SCOP.

For example,
101.1.P.1-1.1cs4.d1cs4a_.sig

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
contacts | Generate intra-chain CON files from CCF files
domainalign | Generate alignments (DAF file) for nodes in a DCF file
domainrep | Reorder DCF file to identify representative structures
domainreso | Remove low resolution domains from a DCF file
interface | Generate inter-chain CON files from CCF files
libgen | Generate discriminating elements from alignments
matgen3d | Generate a 3D-1D scoring matrix from CCF files
psiphi | Calculates phi and psi torsion angles from protein coordinates
rocon | Generates a hits file from comparing two DHF files
rocplot | Performs ROC analysis on hits files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Removes fragment sequences from DHF files
seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generates DHF files from keyword search of UniProt
siggen | Generates a sparse protein signature from an alignment
sigscan | Generates hits (DHF file) from a signature search
sigscanlig | Searches ligand-signature library & writes hits (LHF file)

## 13.0 DIAGNOSTIC ERROR MESSAGES

None.

## 14.0 AUTHORS

Jon Ison (jison © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
Waqas Awan
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references