# Lab Journal - Task 5 (PAH)

## Model calculation

### Modeller

To use Modeller we followed the tutorial written by the students 2011.

• First the target sequence must be provided into PIR-format (2pah has one Lysine at the end and therefore is one aa longer than P00439???):

``` >P1;2pah sequence:2pah:::::::0.00: 0.00 MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR IEVLDNTQQLKILADSINSEIGILCSALQKIK* ```

An example python script for template 1j8u:
Creating the alignment <source lang=python> from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='1j8u.pdb', model_segment=('FIRST:@', 'END:')) aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u') aln.append(file='target.pir', align_codes='2pah') aln.align2d() aln.check() aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR') aln.malign() aln.check() aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR') </source> Single template modeling <source lang=python> from modeller import * from modeller.automodel import * log.verbose() env = environ() a = automodel(env,

```           alnfile  = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',
knowns   = '1j8u',
sequence = '2pah',
assess_methods=(assess.DOPE, assess.GA341))
```

a.starting_model= 1 a.ending_model = 1 a.make() </source>

Also done for 2phm and 3luy.

### Swissmodel

We provide P00439 as query and used advanced options with our three templates 1j8u, 2phm and 3luy alway with chain A.

### I-TASSER

We did following steps on the I-TASSER server for the protein structure and function prediction:

1. Paste query: We set the fasta sequence of our protein PAH (P00439) as query sequence into the big field on the beginning.
2. Paste template (optional): Now, we have three different templates (1J8U, 2PHm and 3LUY) given and so we have to run three different jobs with I-TASSER. Therefore, we type the PDB ID into the field "Specify template without alignment" in `Option I`.
3. Paste cutoff (optional): Since the protein 1J8U has a 100% identity to our protein (2PAH), we did not set any cutoff value for this job. However, we set the cutoff for the PDB ID of 2PHM to 90% and for 3LUY to 35%. For this purpose, one has to set the cutoff in percent in `Option II` into the field "Exclude homologous templates". Subsequent, one can run the job by clicking onto the button "Run I-TASSER.

Since the server is overloaded with jobs, one run takes about 60 hours for completion and everyone can only submit one job!!!

## Model evaluation

The GDT-TS scores were calculated with the LGA server. Following options are used:

```-4 -o2 -gdc -3 -sda
```

Thereby the delivered pdb files are limited to chain A by adding '_A' (for example 2pah_A).

For the calculation of the Cα RMSD we used the sap-script, which can be found on the biolab servers and used as followed:

```/mnt/project/pracstrucfunc13/bin/sap file1.pdb file2.pdb > out.txt
```