ACES: A Co-Evolution Simulator
Using this software, you can create artifical, simulated sequences that display co-evolution signals. These signals, and the conservation of different residues, can be specified in advance. This tool can be used primarily in two ways: to benchmark existing co-evolution detection methods, and to test hypothesis you generated from co-evolution analysis. For example, let's say you observe a co-evolution score for a particular residue pair, but you are worried it is indirect co-evolution. You've noticed that this pair is part of a network of other pairs with significant scores, and this may fully explain the interaction you observe. You can test this directly, by creating simulated sequences that contain this background network but not your pair of interest (or vice-a-versa).
Due to the complexity and processing time involved, this tool is only available as a offline, Java based program. In time, I may list additional resources on this page, such as tools to help generate the input files which contain the constraints. Below, you will find three different iterations of this program: the standard version, with a graphical user interface (aCES1); a command line version, for automated access of the program (aCES-CL); a beta-version of a refined version, in which pools of mutant sequences are generated and selected for (aCES2)
This tool was presented at EB in 2019 - view the abstract, and cite this if you use aCeS in original research.
This tool was also featured in a peer-reviewed article published in the Journal of Bioinformatics and Computational Biology. You can also access the text via research gate or download it directly from this site.
Recommended Citation: Camenares, D (2020) ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences. J Bioinform Comput Biol. 2020 Dec;18(6):2050039. doi: 10.1142/S0219720020500390. Epub 2020 Nov 19.
Offline Files, aCES1
Please select the files you would like to download. The full package includes the manual, an exectuable .jar file, and the soure code.
Offline Files, aCES-CL
Please select the files you would like to download. The full package includes the manual and the soure code (which you can compile to run via command prompt).
Offline Files - aCES2
Please select the files you would like to download. The full package includes the manual, an exectuable .jar file, and the soure code.
Companion Tools
These tools can be useful in conjunction with the ACES software - the first tool, the extractor, will take data on atom position and temperature from a PDB file and report it in an easy to understand and analyze format. Also available for download are Java-based programs that can be used to generate constraints for the ACES program. The first, PDB-2-ACES, will take a PDB file and, given some assumptions regarding the weight to assign to different temperature and occupancies, create co-evolution constraints based upon the structural model. Coming soon - a way to do this with uploaded PDB files (for those created in SwissMODEL, for example). How much should a given residue or position effect be weighed? This can be determined using the PDB extractor and co-evolution analysis. Finally, a similar tool, MSA-2-ACES is available that will take an MSA and from this create the co-evolution constraints that represents the conservation of each residue in the molecule.
*
PDB Information Extractor
This tool can be used to gather atomic level data directly from a PDB file, in a way that makes it easy to calculate and compare residue pair distances and other properties (such as disorder or occupancy). You can check the boxes you'd like to get average residue distance, or atomic level detail, as indicated. They can be displayed as a grid for easy visualization, or as a list for further processing or sorting.
*
MSA Conservation Calculator
This tool will calculate the maximum amount of conservation at a given position. If the 'Display each' button is selected, the amount of any given character along the lenght of the MSA is reported.
PDB-2-ACES
Please select the files you would like to download.
MSA-2-ACES
Please select the files you would like to download.