BMRB NMRSTAR v2.1: In the NMRSTAR v2.1 files the chemical shift assignments should start with a header that explains the data contents. In the following example the necessary tags that ARECA looks for are tagged in an example of NMRSAR v2.1 file: _loop _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 MET CA C 54.400 0.200 1 2 1 MET CB C 33.100 0.200 1 3 1 MET CG C 30.800 0.200 1 4 1 MET HA H 4.180 0.020 1 5 1 MET HB2 H 2.050 0.020 2 6 1 MET HB3 H 2.050 0.020 2 7 1 MET HG2 H 1.920 0.020 2 8 1 MET HG3 H 2.500 0.020 2 9 2 GLN N N 123.047 0.20 1 10 2 GLN H H 8.932 0.02 1 11 2 GLN CA C 55.400 0.200 1 12 2 GLN CB C 29.400 0.200 1 BMRB NMRSTAR v3.1: In this format, the chemical shift assignments should start with a header. An example of the header and the necessary tags for using ARECA is shown. loop_ _Atom_chem_shift.ID _Atom_chem_shift.Temp _Atom_chem_shift.Seq_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Val_err _Atom_chem_shift.Assign_fig_of_merit _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Occupancy _Atom_chem_shift.Details 1 3 3 ARG HA H 1 4.286 0.04 ? 1 ? ? 2 3 3 ARG HB2 H 1 1.801 0.04 ? 2 ? ? 3 3 3 ARG HB3 H 1 1.683 0.04 ? 2 ? ? 4 3 3 ARG HG2 H 1 1.561 0.04 ? 2 ? ? 5 3 3 ARG HG3 H 1 1.517 0.04 ? 2 ? ? 6 3 3 ARG HD2 H 1 3.123 0.04 ? 2 ? ? 7 3 3 ARG HD3 H 1 3.123 0.04 ? 2 ? ? 8 3 3 ARG C C 13 176.261 0.40 ? 1 ? ? 9 3 3 ARG CA C 13 56.230 0.40 ? 1 ? ? 10 3 3 ARG CB C 13 30.760 0.40 ? 1 ? ? 11 3 3 ARG CG C 13 26.990 0.40 ? 1 ? ? 12 3 3 ARG CD C 13 43.320 0.40 ? 1 ? ? 13 4 4 MET H H 1 8.318 0.04 ? 1 ? ? 14 4 4 MET HA H 1 4.392 0.04 ? 1 ? ? 15 4 4 MET HB2 H 1 2.016 0.04 ? 2 ? ? 16 4 4 MET HB3 H 1 1.900 0.04 ? 2 ? ? XEASY: Since the amino acid types are not reported in the XEASY chemical shift assignment format, to run ARECA the users need to upload a sequence file. Examples of the chemical shift and sequence files are shown: Example of an assignment file (the assignment file should be provided in a plain text file; other file formats such as rtf, doc, docx, xls, or pdf contain additional header/footer): 1 4.286 0.000 HA 1 2 1.801 0.000 HB2 1 3 1.683 0.000 HB3 1 4 1.561 0.000 HG2 1 5 1.517 0.000 HG3 1 6 3.123 0.000 HD2 1 7 3.123 0.000 HD3 1 8 176.261 0.000 C 1 9 56.230 0.000 CA 1 10 30.760 0.000 CB 1 11 26.990 0.000 CG 1 12 43.320 0.000 CD 1 13 8.318 0.000 H 2 14 4.392 0.000 HA 2 15 2.016 0.000 HB2 2 16 1.900 0.000 HB3 2 Sequence file: The sequence file should contain 1 amino acid per line, without header or footer tags. The three letter codes should be used. ARG MET ASP ASN THR GLU LEU PONDEROSA: Peak picking of the NOESY spectra is usually a challenging process. In these cases, the PONDEROSA Client can be used that gets the spectra as inputs and performs an automatic peak picking. ARECA accepts the packed_inputs.txt file that is the output of PONDEROSA Client. When the packed file is uploaded the users do not need to upload the chemical shift assignments file nor the peak lists.
The peak lists could be in the SPARKY or XEASY formats. When more than one peak lists for the 13C-NOESY are uploaded (ali, aro, d2o), the column arrangement of the ω1, ω2, and ω3 are the same. Even though accepted, it is recommended to provide the peak heights. peak lists in the SPARKY format Assignment w1 w2 w3 Data Height ?-?-? 0.52 117.83 8.36 859602.00 ?-?-? 0.70 121.77 7.81 196283.00 ?-?-? 0.98 122.16 8.95 325603.00 peak lists in the XEASY format # Number of dimensions 3 #INAME 1 C #INAME 2 H #INAME 3 HC #CYANAFORMAT ChH 1 53.430 3.406 4.826 1 U 0.728E+08 0.000E+00 e 0 0 0 0 2 53.430 3.666 4.824 1 U 0.846E+08 0.000E+00 e 0 0 0 0
ARECA is capabale of validating different portions of the chemical shift assignments based on the different types of NMR studies. Fig.1. shows the different analyses that ARECA performs.
