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  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  program.
Three different formats of the sequence-structure alignment data are accepted by the server (see examples below).
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
aa1 n1 aa2 n2
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
Example (SAL format)
Model1 1wdn_A Query: RKNGLNVKMDYTPNSGQLVRNLLNGKYNIAVAGIDNVIAYQEGQVKEPVVNPDMFAFYGV Sbjct: KELKLDYELKP-MDFSGIIPALQTKNVDLALAGITIT--------DERKKAIDFSDGYYK Query: DNGLLSLVA-NPQIKNISDLKGKQVSVDALTTG Sbjct: SGLLVMVKANNNDVKSVKDLDGKVVAVKSGTGS
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:  A. Zemla (1998) AL2TS - Translate sequence-structure alignment (AL) into tertiary structure (TS): Accessed at http://predictioncenter.llnl.gov/local/al2ts/al2ts.html  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).  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.