Dear Tasneem Harahsheh,

It is important to realise that your question is like finding the holy grail of protein science. Only X-ray and NMR techniques are able to give a reasonable certainty about the 3D structure.

However to get an idea you could try one of the best 3D prediction programs available:

I-Tasser.

https://zhanglab.ccmb.med.umich.edu/I-TASSER/

https://www.researchgate.net/publication/270290593_The_I-TASSER_suite_Protein_structure_and_function_prediction

For interesting background information regarding aptamers and bioinformatics see:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751119/

What might be useful for you very much depends on what you have in terms of possibilities (MD programs etc.), the kind of protein and aptamer, what you exactly want to know.

What you are looking for might possibly be:

AptaMetrics

https://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(16)32957-4

AptaSUITE

https://www.cell.com/molecular-therapy-family/nucleic-acids/fulltext/S2162-2531(18)30050-7

Possibly also:

https://arxiv.org/ftp/arxiv/papers/1711/1711.07397.pdf

Hope this is of any help to you.

Hi,

You can use SWISS-MODEL (https://swissmodel.expasy.org) and I-Tasser for free software to predict your protein structure. They predict the structure based on similar templates structures available and you can visualise the predicted protein structure by using PyMOL

PEP-FOLD 3 is a de novo approach aimed at predicting peptide structures from amino acid sequences. This method based on structural alphabets that describe the conformations of 4 consecutive structural alphabets, Coupling of predicted series of alphabets to the algorithm and Coarse-grained force field.

Also CPH models and PHYRE2 can be used where former uses neural network and later uses HMM-Hidden Markov Models to predict the structure with higher accuracy.

Hi Tasneem Harahsheh,

The 3D structure of any protein sequence can be predicted by PyMol (http://www.pymol.org/), UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/) and Antheprot 3D (https://www.antheprot-pbil.ibcp.fr) by inputting the PDB file of the polypeptide sequence.

Hi Tasneem,

You can try SWISS-MODEL (https://swissmodel.expasy.org) or PyMol (http://www.pymol.org/) for preliminary predictions, but if you want to know the exact interaction sites, then structural biology technologies, including X-ray crystallography, NMR, and cryo-electron microscopy technology must be used to solve this problem. Recommend an article for you, maybe can help you choose experimental method to determine the structure, https://www.creative-biostructure.com/comparison-of-crystallography-nmr-and-em_6.htm

Hope it helps!

You can refer to below attached paper full-text, which has all the methodology detials and link to webservers.