PrOCoil - Predicting the Oligomerization of Coiled Coil Proteins

We 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. All data used for evaluating the computational approach and for training the final models are available for download.

How to cite PrOCoil

If 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

Web service

Enter your coiled coil sequence here:

MKQLEDKVEELLSKNYHLENEVARLKKLV abcdefgabcdefgabcdefgabcdefga

Accept PairCoil2 output format

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.

If you are studying a new amino acid sequence for which no coiled coil annotation is available, you can use a coiled coil predictor to create the necessary annotation.

1. If you use PairCoil2, view the "Positions and register" output and paste the lines containing the sequence and the register to the above input field. Tick "Accept PairCoil2 output format" to ensure that the data are correctly interpreted.
2. If you use Marcoil, you cannot use the above input field directly. Instead, paste Section "3. LIST WITH [COILED-COIL PROBABILITY IN PERCENT] AND HEPTAD PHASE WITH HIGHEST PROBABILITY" of the Marcoil output into the following text box:

1M[00.0]e 2G[00.0]f 3E[00.1]g 4C[00.1]a 5D[00.1]b 6Q[00.1]c 7L[00.1]d 8L[00.1]e 9V[00.1]f 10F[00.1]g 11M[00.1]a 12I[00.2]b 13T[00.2]c 14S[00.3]d 15R[00.6]e 16V[00.7]f 17L[01.0]g 18V[01.4]a 19L[01.6]b 20S[02.3]c 21T[03.0]d 22L[04.0]e 23I[05.3]f 24I[08.8]g 25M[16.4]a 26D[20.8]b 27S[23.2]c 28R[25.4]d 29Q[33.2]e 30V[36.5]f 31Y[43.7]g 32L[73.8]a 33E[85.1]b 34N[88.6]c 35L[91.3]d 36R[92.0]e 37Q[92.4]f 38F[92.7]g 39A[95.4]a 40E[97.5]b 41N[98.2]c 42L[98.7]d 43R[98.8]e 44Q[98.9]f 45N[98.9]g 46I[99.0]a 47E[99.0]b 48N[99.0]c 49V[99.0]d 50H[98.9]e 51S[98.9]f 52F[98.9]g 53L[99.0]a 54E[99.1]b 55N[99.1]c 56L[99.1]d 57R[99.0]e 58A[99.0]f 59D[98.9]g 60L[98.8]a 61E[98.4]b 62N[97.3]c 63L[95.6]d 64R[90.5]e 65Q[82.3]f 66K[64.9]g 67F[27.0]a 68P[05.3]b 69G[02.2]c 70K[00.8]d 71W[00.1]e 72Y[00.0]f 73S[00.0]g 74A[00.0]a 75M[00.0]b 76P[00.0]c 77G[00.0]d 78R[00.0]e 79H[00.0]f 80G[00.0]g

Probability cut-off: %

© 2006 by Institute of Bioinformatics, Johannes Kepler University Linz, A-4040 Linz, Austria [view imprint]