Institute of Bioinformatics

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.

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. The updated data sets and some information on how they have been collected are available from the PrOCoil Data Repository (v2). If you want to use the original 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 sets on which the original PrOCoil models were based are still available from the PrOCoil Data Repository (v1).

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

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.

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.
If you use Marcoil, you cannot use the above input field directly. Instead, go to the "Prob List" tab of the Marcoil results and click "Export". Then copy the four-column table with residue numbers, residues, probabilities, and most probable heptad positions (see sample input below) and paste it into the text field below:

1 M   0.0 e 
   2 G   0.0 f 
   3 E   0.1 g 
   4 C   0.1 a 
   5 D   0.1 b 
   6 Q   0.1 c 
   7 L   0.1 d 
   8 L   0.1 e 
   9 V   0.1 f 
  10 F   0.1 g 
  11 M   0.1 a 
  12 I   0.2 b 
  13 T   0.2 c 
  14 S   0.3 d 
  15 R   0.6 e 
  16 V   0.7 f 
  17 L   1.0 g 
  18 V   1.4 a 
  19 L   1.6 b 
  20 S   2.3 c 
  21 T   3.0 d 
  22 L   4.0 e 
  23 I   5.3 f 
  24 I   8.8 g 
  25 M  16.4 a 
  26 D  20.8 b 
  27 S  23.2 c 
  28 R  25.4 d 
  29 Q  33.2 e 
  30 V  36.5 f 
  31 Y  43.7 g 
  32 L  73.8 a 
  33 E  85.1 b 
  34 N  88.6 c 
  35 L  91.3 d 
  36 R  92.0 e 
  37 Q  92.4 f 
  38 F  92.7 g 
  39 A  95.4 a 
  40 E  97.5 b 
  41 N  98.2 c 
  42 L  98.7 d 
  43 R  98.8 e 
  44 Q  98.9 f 
  45 N  98.9 g 
  46 I  99.0 a 
  47 E  99.0 b 
  48 N  99.0 c 
  49 V  99.0 d 
  50 H  98.9 e 
  51 S  98.9 f 
  52 F  98.9 g 
  53 L  99.0 a 
  54 E  99.1 b 
  55 N  99.1 c 
  56 L  99.1 d 
  57 R  99.0 e 
  58 A  99.0 f 
  59 D  98.9 g 
  60 L  98.8 a 
  61 E  98.4 b 
  62 N  97.3 c 
  63 L  95.6 d 
  64 R  90.5 e 
  65 Q  82.3 f 
  66 K  64.9 g 
  67 F  27.0 a 
  68 P   5.3 b 
  69 G   2.2 c 
  70 K   0.8 d 
  71 W   0.1 e 
  72 Y   0.0 f 
  73 S   0.0 g 
  74 A   0.0 a 
  75 M   0.0 b 
  76 P   0.0 c 
  77 G   0.0 d 
  78 R   0.0 e 
  79 H   0.0 f 
  80 G   0.0 g

Probability cut-off: %