AL2TS

Format Description

The AL2TS server translates sequence-structure alignment data into standard PDB atom records (coordinates). The document below describes the format of sequence-structure alignment acceptable by the AL2TS facility. This service is the extended version of the server [1] developed to facilitate Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments.

Each alignment model is automatically translated into TS format where the backbone atom coordinates from the selected PDB entry are assigned to corresponding residues from the model.

Notes:
  - assigned atoms contain "1.0" in the occupancy field
  - assigned atoms contain "0.0" in the temperature factor field
  - only N, CA, C, and O atoms are reported (default option)

Side chain building can be performed by selecting SCWRL option or using SCWRL [2] program.
When SCWRL option is selected, then side chain atom positions are calculated for all residues in the model. By selecting IDres+SCWRL option the identical residues are copied from the template (STATIC_FRAME) to the model, and the Scwrl program is used to calculate side chain atom positions for remaining residues only.

Three different formats of the sequence-structure alignment data are accepted by the server (see examples below).

AL format of the alignment data (AL):

The input data should begin with PARENT and end with TER record.

PARENT - Specifies PDB entry used by AL model
    e.g. PARENT 1abc_A
           Indicates that the model or the independent segment of
           structure is based on a single PDB entry 1abc chain A
           (use _A to indicate chain A).
    NOTE1: Specifying NMR MODEL please use the following notation: 
           1bve_B_5   for PDB entry: 1bve, chain: 'B', model: 5 
           1awo___7   for PDB entry: 1awo, chain: ' ', model: 7
           (otherwise the first MODEL will be used as a template).
    NOTE2: The code must correspond to a current PDB entry.

TER    - Terminates independent segments of structure in the AL model

The (four column) alignment data records provide: model residue name (one letter symbol), model residue sequence number, PDB residue name (one letter symbol), and PDB residue sequence number with an insertion code if necessary:
```
    aa1 n1  aa2 n2
```
No model residue may be repeated in the alignment

Example (AL format)

PARENT 1ppf_E
S   5    V   62
Q   6    N   63
T   7    V   63A
C   8    R   63B
Y   9    A   63C
N  10    V   64
S  11    R   65
TER
PARENT 1bdb_A
E  17    L  249
T  18    N  250
V  19    Y  251
D  20    D  252
G  21    G  253
R  22    G  254
A  23    L  255
L  24    G  256
K  25    V  257
TER

Sequence format of the alignment data (SAL):

All records of SAL format data for AL2TS facility should begin with 'Query:' or 'Sbjct:' keywords followed by a space ' ' as a separator.
Both lines in a pair 'Query:' and 'Sbjct:' should contain the same number of characters.
Keywords 'Query:' and 'Sbjct:' are case sensitive. Please type carefully.

Example (SAL format)

Model1
1wdn_A

Query: RKNGLNVKMDYTPNSGQLVRNLLNGKYNIAVAGIDNVIAYQEGQVKEPVVNPDMFAFYGV
Sbjct: KELKLDYELKP-MDFSGIIPALQTKNVDLALAGITIT--------DERKKAIDFSDGYYK

Query: DNGLLSLVA-NPQIKNISDLKGKQVSVDALTTG
Sbjct: SGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGS

Sequence format of the alignment data (BLAST):

This format is included to the service to make your life easier when you already have sequence-structure alignment results from BLAST or PSI-BLAST programs (see examples below).

Example (BLAST format [3])

Model2
1rdr_A 

Query: 1   DKGFVLGH-SITDVTFLKRHFHMDYGTGF-YKPVMASKTLEAILSFAR-RGTIQEKLISV 57
           DK       +  +VTFLKR F  D    F   PVM  K +   + + +     Q+ + S+
Sbjct: 358 DKSATFETVTWENVTFLKRFFRADEKYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSL 417

Query: 58  AGLAVHSGPDEYRRLFEPFQGLFE-----IPSYRSLYLRWVNA 95
             LA H+G +EY +     + +       +P Y +LY RW+++
Sbjct: 418 CLLAWHNGEEEYNKFLAKIRSVPIGRALLLPEYSTLYRRWLDS 460

References: 

[1] A. Zemla (1998) AL2TS - Translate sequence-structure alignment (AL) into 
    tertiary structure (TS): Accessed at
    http://predictioncenter.llnl.gov/local/al2ts/al2ts.html
 
[2] M. Bower, F. E. Cohen, and R. L. Dunbrack, Jr. Sidechain prediction 
    from a backbone-dependent rotamer library: A new tool 
    for homology modeling. J. Mol. Biol. 267, 1268-1282 (1997).  

[3] Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., 
    Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new 
    generation of protein database search programs. Nucleic Acids Res 25(17), 
    3389-3402.