PrOCoil - Predicting the Oligomerization of Coiled Coil ProteinsWe have developed an SVM-based classification method for predicting whether a given coiled coil sequence is a trimer or dimer (assuming that it is one of both). This method also allows for a deep analysis of the sequence which residues are mainly responsible for the outcome. The software is available as an R package and as a simple-to-use Web application (see below). See the user manual for details about both variants.
Important Note: the prediction models of the PrOCoil Web application have been updated along with the release of version 2.0.0 of the PrOCoil R package. If you want to use the prediction models as published by Mahrenholz et al. (2011), you have to use the PrOCoil R package. For details, please follow the instructions in Section 5.5.3 of the user manual. The data provided on the PrOCoil data page are still the data on which the previous models were trained. An update of the data and a publication about PrOCoil v2 are currently in preparation.
How to cite PrOCoilIf you use PrOCoil for research that is published later, you are kindly asked to cite it as follows:
C. C. Mahrenholz, I. G. Abfalter, U. Bodenhofer, R. Volkmer, and S. Hochreiter. Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics 10(5):M110.004994, 2011. DOI: 10.1074/mcp.M110.004994
Required input format: amino acid sequence (uppercase letters "A" - "Z"; non-standard letters "B", "J", "O", "U", "X" and "Z" are accepted, but ignored) and an annotation of the same length consisting of lowercase letters "a"-"g" (denoting the heptad registers of coiled coil seqments) or dashes "-" (denoting non-coiled coil amino acids). The symbols "a"-"g" should be in proper order ("a" followed by "b", "b" followed by "c", ..., "g" followed by "a"), but heptad irregularities are accepted as well. All whitespaces are ignored. If you tick "Accept PairCoil2 output format", all digits are stripped and dots are converted into dashes (to comply with the PairCoil2 "Positions and registers"output). PrOCoil also allows for comparative analysis of two aligned sequences with a common heptad register. In order to do that, supply the second sequence underneath the heptad register. Only one data record (sequence + annotation [+ sequence]) can be submitted at at time.