PROFASI  Version 1.5
Accepted sequence input format in PROFASI

The sequence information can be given in spelled out residue names (if it is a single word), 3 letter codes or one letter codes. By default, sequence reading starts in the word mode: either 3 letter codes or full names. If the character "*" (asterix) is encountered, the reading mode toggles between word and one letter code modes. So, *VAL VAL* is the sequence V-A-L-V-A-L, and VAL VAL is the sequence V-V. If there are capping groups, like Acetyl (ACE), they can be specified with their names or 3-letter codes.

Other possible capping groups are C-terminal amide (NH2) or N-methyl (NME) and the N-terminal Succinylic acid (SUC) and the "VoidEG". The VoidEG (written like that in the sequence for PROFASI) takes the place of a capping group, but does not add anything there. This forces the program to start the chain at the N-terminus with a NH-Calpha... instead of a charged N terminus with 3 hydrogens. In other words, the residue at the N-terminal is treated as if it were in some other location on the chain. VoidEG can be attached also at the C-terminus for a similar effect.

As a contrived example, let's consider a peptide Acetyl-ACDEFGHI-(D-proline)-KLMNPQRSTVWY. Let's also imagine that for some reason we want the C-terminal Y to behave as if it was in the middle of a chain: i.e., no COO(-) ending. In the settings file for simulation programs, we would enter this sequence as:

add_chain 1 < ACE *ACDEFGHI *DPR* KLMNPQRSTVWY *VoidEG>

We start writing in the "word mode" and enter ACE for Acetyl. Then with the "*" we toggle to the "letter mode" and enter the sequence Alanine (A), Cysteine (C), Aspartic acid (D) ... up to Isoleucine (I). Then we need D-proline which does not have a single character code like natural amino acids. So, we use the "*" to toggle to the word mode and enter its 3-letter code DPR, and toggle back to the letter mode for the regular amino acids. Then we continue with Lysine (K), Leucine (L) ... until Tyrosine (Y). We switch to the word mode again and name the special capping group VoidEG which fakes the presence of a capping group for the chain constructor routines without adding any atom.


PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2