31.1 INTRODUCTION

Protein folding is dictated by the physical forces acting on the atoms of the protein. In general, the most accurate way of formulating the protein‐folding or structure prediction problem is in terms of an all‐atom model subject to the physical forces. Energy functions compatible with the protein representation are considered during the ab initio approach. Faster algorithms are developed to search the best‐fitting formation, in order to minimize the energy function while predicting the tertiary structure ab initio.

31.2 OBJECTIVE

To predict the tertiary structure of a peptide using an ab initio approach with the online tool RaptorX.

31.3 PROCEDURE (RAPTORX)

1. Suppose we need to predict the structure of the given protein sequence (Bubaline Dicer I; NCBI Protein Accession Number BAP00765.1): >BAP00765|Bbu_Dicer1

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2. Open RaptorX: http://raptorx.uchicago.edu/
3. Click on the “Submit” button in the first server option “RaptorX structure prediction”, or directly paste this uniform resource locator (URL) in the space for the URL: http://raptorx.uchicago.edu/StructurePrediction/predict/
4. Type your job identification and email in the respective spaces, as shown in the previous chapter (Figure 30.1).
5. Paste the input sequence (in FASTA format) in the sequence box under “Sequences for Prediction”.

31.4 JOB STATUS

Once the job has been started, the status can be seen in real time on the screen as below:

31.5 OUTPUT AND INTERPRETATION OF RESULTS

Open the specified email ID to get the results:

1. Predicted structure in *.png format.
2. Predicted structure in *.pdb format.
3. Ligand binding site detail as *domain_pocket.txt file.

Click on the link provided in the mail to open the detailed result in a new window.

31.5.1 Section I: input sequence and domain partition

The whole protein sequence is partitioned into domains (here six domains), depending on the available template structures in PDB. The domains are indicated by assigning a domain number in every third row of sequence blocks.

31.6 QUESTIONS

1. 1. Predict the tertiary structure of the caprine beta‐defensin (GenBank Acc. No. ABF71365.1) using an ab initio approach
2. 2. Predict the tertiary structure of the same peptide (caprine beta‐defensin) by homology modeling, using a human homolog.
3. 3. Can you compare the results obtained from the above two methods?
4. 4. What parameters are considered in RaptorX for determining the goodness of the predicted structure?