Does anyone know what the best software (open-source if possible) to generate consistent and exhaustive multiple short peptide structures (2-6 aminoacidic moieties) is? I realize there will be a lot of codes for generating sequences through letters and then convert them into 3D structures, but they can't be systematic enough to cover all possibilites.
Some months ago I faced with this question. After a lot of search, I found the best software for this purpose is pymol software and also is freeware.
When you open it, there are two panels. In the above one, there is a button in the right with the name of builder. In that part you find a button for protein. When you click on it, you will see amino acids names. I hope this help you.
That's cool, I had no idea of this approach, although I was looking for something for automatic rather than manual.
However, as I was in rush to do so, I finally used another approach, consisting in building the peptide sequence based on SMILES notation, where the repeating pattern corresponds to
1st residue/ => NC(=O)[C@H] ()
2nd residue/ => NC(=O)[C@H]()
3rd residue/ => NC(=O)[C@H]()
....
where the '()' delimits the location where the side-chain of each residue must be written in SMILES format. Doing so, afterwards concatenating the residues in a sequential manner, you create a SMILES string, and then, with babel command line, you can easily convert to a 3D PDB file (at most, only 5-6 residues can be converted, if you desire longer poly-peptide chains, another option should be used).
The way I converted from smiles to pdb, is as easy as below:
babel --gen3d -h -ipdb seq.smi -opdb seq.pdb
Everything was built with open-source software, in case someone else needs to do something similar, this is the alternative (although more tricky way) to do so. The main advantage, is you can insert within the '()' any sidechain, and you can create consistently and sistematically every poly-peptide of lenght N very easily.
That was interesting. Thank you for your great way. I should use it in my work.
Today I read your answer about analysis of docking poses. I encountered with a question. Which software can I use for re scoring my ligand poses based on mmff94 force field?
I recommend to use MOE software, which unfortunately is not free for academics. I used long time ago and it rendered very good correlations between experimental energy and the predicted docking energy after local minimization of docked pose.
Nowadays, I'm not aware of any other software that could use such FF for docking minimization, sorry, but I realized that using Autodock Vina in conjunction with NNScore (developed by Durrant et al) for re-scoring is rendering reasonable values of energy.
But is up to you to test any alternative approach. I recommend to read a really nice paper (Latest developments in molecular docking: 2010-2011 in review, from Elizabeth Yuriev et al, at J. Mol. Recognit, 2013), where many different alternative docking protocols are described herein.
Best regards!!
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