Alignment File Creation

Alignment File Creation for Homology Model

The In.pdb file is a structure (homologous to the protein of our interest) for which we know the primary amino acid sequence. This is the template structure for Modeller. The Out.pdb file is the structure of the protein we are interested in. We know the primary amino acid sequence of the protein we are interested but do not know the 3D shape.

• Get FASTA sequences for both the template and target structure form uniprot.

• Paste sequences into Clustar Omega and generate an alignement (FASTA).

• Save the template file as In.pdb.

• Find the beginning and end portions of the sequence in the In.pdb file. Cut out any portion on the ali file that is outside of the pdb file's range (these are missing residues). In place of the missing residues that were deleted add one slack to indicate a chain break. Note: Any part you cut out of the template portion of the alignment, you must also cut out of the structure portion.

• Change the alignment to match this format:

>P1;In
structureX:In: 1:A : 1451:A :undefined:undefined:-1.00:-1.00
MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDREL
ASKKNPKLINALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIAIYL
GIGLCLLFIVRTLLLHPAIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSN
NLNKFDEGLALAHFVWIAPLQVALLMGLIWELLQASAFCGLGFLIVLALFQAGLGRMMM
KYRDQRAGKISERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAAYVRYFN
SSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVLRMAVTRQFPWAVQTWYDSLGAINKI
QDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELF/LLGTPVLKDINFKIERGQLLAVA
GSTGAGKTSLLMVIMGELEPSEG
*

>P1;Out
sequence:Out: 1:A : 1451:A :undefined:undefined:-1.00:-1.00
MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDREL
ASKKNPKLINALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIAIYL
GIGLCLLFIVRTLLLHPAIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSN
NLNKFDEGLALAHFVWIAPLQVALLMGLIWELLQASAFCGLGFLIVLALFQAGLGRMMM
KYRDQRAGKISERLVITSEMIENIQSVKAYCWEEAMEKMIENLRQTELKLTRKAAYVRYFN
SSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVLRMAVTRQFPWAVQTWYDSLGAINKI
QDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELF/LLGTPVLKDINFKIERGQLLAVA
GSTGAGKTSLLMVIMGELEPSEG
*

• Note: each sequence ends with a * and you have the appropriate headers. The header, StructureX:(In), msut be the title of the pdb file. '1:A' means the pdb file means the pdb file starts at amino acid 1 on chain A and the '1451:A' means the sequence ends at chain A on amino acid 1451. (There are less than 1451 residues in the sequence, I do not want the box to be too large).

• Note: when you use models without abnormal residues as template to generate new models, you should replace abnormal residues with dash in your alignment file.