NetSurfP - 1.1

Protein secondary structure and relative solvent accessibility

The NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence.
The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.

Submission

CITATIONS

For publication of results, please cite:

A generic method for assignment of reliability scores applied to solvent accessibility predictions.
Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen and Claus Lundegaard¹.
BMC Structural Biology 2009, 9:51 doi:10.1186/1472-6807-9-51.

The electronic version of this article is found here: download

Instructions

1. Specify the input sequences

All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:

A C D E F G H I K L M N P Q R S T V W Y

The sequences can be input in the following two ways:

Paste a single sequence (just the amino acids) or a number of sequences in FASTA format into the upper window of the main server page.
Select a FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.

2. pipes

All pipes '|' will be replaced with an underscore '_' in the name of a fasta-entry eg:

>test|something
ELVISLEVER

is replaced by

>test_something
ELVISLEVER

3. Lowercase letters

All lowercase letters in a sequence will be changed to uppercase letters

4. Submit the job

Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.

Output format

>2WNS.A.1 TRANSFERASE
ALGPLVTGLYDVQAFKFGDFVLKSGLSSPIYIDLRGIVSRPRLLSQVADILFQTAQNAGIS
FDTVCGVPYTALPLATVICSTNQIPMLIRRKETKDYGTKRLVEGTINPGETCLIIEDVVTS
GSSVLETVEVLQKEGLKVTDAIVLLDREQGGKDKLQAHGIRLHSVCTLSKMLEILEQQKKV
DAETVGRVKRFIQE

A prediction using the sequence 2WNS.A.1 will give the following output:


# For publication of results, please cite:
# A generic method for assignment of reliability scores applied to solvent accessibility predictions.
# Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen and Claus Lundegaard
# BMC Structural Biology 2009, 9:51 doi:10.1186/1472-6807-9-51
#
# Column 1: Class assignment - B for buried or E for Exposed - Threshold: 25% exposure, but not based on RSA
# Column 2: Amino acid
# Column 3: Sequence name
# Column 4: Amino acid number
# Column 5: Relative Surface Accessibility - RSA
# Column 6: Absolute Surface Accessibility
# Column 7: Z-fit score for RSA prediction
# Column 8: Probability for Alpha-Helix
# Column 9: Probability for Beta-strand
# Column 10: Probability for Coil
E A  2WNS.A.1               1    0.777  85.680   1.547   0.003   0.003   0.994
E L  2WNS.A.1               2    0.281  51.451   0.503   0.802   0.014   0.185
E G  2WNS.A.1               3    0.530  41.687   1.558   0.938   0.007   0.055
E P  2WNS.A.1               4    0.549  77.846   2.101   0.938   0.007   0.055
B L  2WNS.A.1               5    0.074  13.531   0.513   0.938   0.007   0.055
B V  2WNS.A.1               6    0.068  10.405   1.064   0.975   0.003   0.022
E T  2WNS.A.1               7    0.538  74.662   2.087   0.975   0.003   0.022
E G  2WNS.A.1               8    0.296  23.335   2.326   0.970   0.001   0.030
B L  2WNS.A.1               9    0.029   5.310   0.164   0.970   0.001   0.030
E Y  2WNS.A.1              10    0.326  69.581   1.270   0.923   0.002   0.076
E D  2WNS.A.1              11    0.764 110.107   1.486   0.782   0.003   0.216
B V  2WNS.A.1              12    0.217  33.307   1.603   0.321   0.003   0.675
E Q  2WNS.A.1              13    0.563 100.516   0.817   0.018   0.019   0.964
B A  2WNS.A.1              14    0.058   6.348   0.220   0.018   0.088   0.893
B F  2WNS.A.1              15    0.088  17.662   0.307   0.022   0.552   0.426
E K  2WNS.A.1              16    0.370  76.150   0.997   0.022   0.552   0.426
E F  2WNS.A.1              17    0.454  91.178   0.204   0.021   0.451   0.528
E G  2WNS.A.1              18    0.387  30.481  -0.578   0.019   0.141   0.840
E D  2WNS.A.1              19    0.574  82.742   0.151   0.019   0.141   0.840
B F  2WNS.A.1              20    0.126  25.288   0.725   0.021   0.756   0.223
E V  2WNS.A.1              21    0.393  60.373   0.761   0.018   0.846   0.136
B L  2WNS.A.1              22    0.155  28.289   0.530   0.018   0.846   0.136
E K  2WNS.A.1              23    0.502 103.323   0.020   0.022   0.552   0.426
B S  2WNS.A.1              24    0.319  37.352  -1.215   0.020   0.205   0.775
E G  2WNS.A.1              25    0.502  39.500  -1.743   0.019   0.141   0.840
E L  2WNS.A.1              26    0.384  70.237  -0.338   0.021   0.279   0.699
E S  2WNS.A.1              27    0.449  52.658  -0.193   0.021   0.451   0.528
B S  2WNS.A.1              28    0.158  18.564  -0.225   0.022   0.359   0.619
E P  2WNS.A.1              29    0.452  64.110  -0.834   0.021   0.279   0.699
B I  2WNS.A.1              30    0.232  42.883   0.867   0.023   0.655   0.322
B Y  2WNS.A.1              31    0.115  24.554   0.056   0.021   0.756   0.223
B I  2WNS.A.1              32    0.163  30.155   1.405   0.021   0.756   0.223
B D  2WNS.A.1              33    0.170  24.439  -1.081   0.074   0.484   0.442
B L  2WNS.A.1              34    0.127  23.180   0.923   0.118   0.150   0.732
E R  2WNS.A.1              35    0.377  86.425   0.324   0.278   0.093   0.628
E G  2WNS.A.1              36    0.367  28.883   0.146   0.354   0.048   0.598
B I  2WNS.A.1              37    0.099  18.389  -0.147   0.354   0.048   0.598
B V  2WNS.A.1              38    0.204  31.293  -1.012   0.257   0.016   0.727
E S  2WNS.A.1              39    0.511  59.831  -0.779   0.058   0.017   0.925
B R  2WNS.A.1              40    0.270  61.807   0.663   0.058   0.017   0.925
B P  2WNS.A.1              41    0.212  30.140  -0.022   0.923   0.002   0.076
E R  2WNS.A.1              42    0.603 138.133   1.212   0.970   0.001   0.030
B L  2WNS.A.1              43    0.095  17.340   0.474   0.970   0.001   0.030
B L  2WNS.A.1              44    0.036   6.518   0.464   0.970   0.001   0.030
E S  2WNS.A.1              45    0.352  41.219   1.396   0.970   0.001   0.030
E Q  2WNS.A.1              46    0.301  53.776   1.768   0.970   0.001   0.030
B V  2WNS.A.1              47    0.020   3.105   1.269   0.970   0.001   0.030
B A  2WNS.A.1              48    0.026   2.898   0.818   0.970   0.001   0.030
E D  2WNS.A.1              49    0.440  63.462   1.892   0.970   0.001   0.030
B I  2WNS.A.1              50    0.165  30.451   1.468   0.970   0.001   0.030
B L  2WNS.A.1              51    0.021   3.790   1.276   0.970   0.001   0.030
B F  2WNS.A.1              52    0.072  14.430   0.645   0.970   0.001   0.030
E Q  2WNS.A.1              53    0.585 104.463   1.979   0.970   0.001   0.030
B T  2WNS.A.1              54    0.179  24.786   1.814   0.970   0.001   0.030
B A  2WNS.A.1              55    0.030   3.284   0.243   0.970   0.001   0.030
E Q  2WNS.A.1              56    0.511  91.318   1.607   0.923   0.002   0.076
E N  2WNS.A.1              57    0.836 122.376   0.971   0.782   0.003   0.216
E A  2WNS.A.1              58    0.422  46.493   0.522   0.321   0.003   0.675
E G  2WNS.A.1              59    0.667  52.501  -1.111   0.016   0.005   0.979
B I  2WNS.A.1              60    0.173  32.060   0.007   0.003   0.003   0.994
E S  2WNS.A.1              61    0.636  74.551   1.229   0.005   0.045   0.951
B F  2WNS.A.1              62    0.086  17.320   1.054   0.004   0.197   0.799
E D  2WNS.A.1              63    0.309  44.556   0.085   0.004   0.514   0.481
B T  2WNS.A.1              64    0.074  10.278   0.703   0.001   0.959   0.040
B V  2WNS.A.1              65    0.018   2.720   0.753   0.001   0.959   0.040
B C  2WNS.A.1              66    0.023   3.159   1.210   0.001   0.959   0.040
B G  2WNS.A.1              67    0.037   2.880  -0.003   0.004   0.616   0.381
B V  2WNS.A.1              68    0.054   8.346   1.111   0.005   0.336   0.660
E P  2WNS.A.1              69    0.282  40.087   0.666   0.018   0.088   0.893
E Y  2WNS.A.1              70    0.300  64.003  -0.940   0.115   0.016   0.868
E T  2WNS.A.1              71    0.350  48.600  -1.088   0.176   0.004   0.820
B A  2WNS.A.1              72    0.082   9.003  -2.119   0.321   0.003   0.675
B L  2WNS.A.1              73    0.111  20.361   0.710   0.802   0.014   0.185
B P  2WNS.A.1              74    0.182  25.868   0.084   0.879   0.010   0.111
B L  2WNS.A.1              75    0.104  19.061   0.708   0.938   0.007   0.055
B A  2WNS.A.1              76    0.018   2.006   0.770   0.975   0.003   0.022
B T  2WNS.A.1              77    0.136  18.905   0.910   0.970   0.001   0.030
B V  2WNS.A.1              78    0.151  23.147  -0.019   0.970   0.001   0.030
B I  2WNS.A.1              79    0.041   7.622   0.643   0.988   0.000   0.012
B C  2WNS.A.1              80    0.019   2.640   0.490   0.970   0.001   0.030
E S  2WNS.A.1              81    0.413  48.357   1.221   0.970   0.001   0.030
E T  2WNS.A.1              82    0.431  59.835   0.411   0.923   0.002   0.076
B N  2WNS.A.1              83    0.175  25.664   0.553   0.600   0.003   0.397
E Q  2WNS.A.1              84    0.850 151.774  -0.347   0.016   0.005   0.979
B I  2WNS.A.1              85    0.089  16.410   0.916   0.005   0.015   0.979
E P  2WNS.A.1              86    0.336  47.664  -0.069   0.004   0.138   0.858
B M  2WNS.A.1              87    0.043   8.504   0.261   0.001   0.900   0.099
B L  2WNS.A.1              88    0.034   6.207   0.142   0.001   0.959   0.040
B I  2WNS.A.1              89    0.059  10.878   0.533   0.001   0.959   0.040
B R  2WNS.A.1              90    0.042   9.641  -0.492   0.001   0.900   0.099
B R  2WNS.A.1              91    0.189  43.327   1.011   0.003   0.718   0.279
E K  2WNS.A.1              92    0.320  65.865   0.874   0.004   0.420   0.576
E E  2WNS.A.1              93    0.658 114.918   1.306   0.019   0.141   0.840
E T  2WNS.A.1              94    0.696  96.535  -0.161   0.018   0.047   0.935
E K  2WNS.A.1              95    0.583 119.944  -0.149   0.018   0.088   0.893
E D  2WNS.A.1              96    0.676  97.484  -0.016   0.020   0.205   0.775
E Y  2WNS.A.1              97    0.362  77.274  -0.164   0.021   0.279   0.699
E G  2WNS.A.1              98    0.371  29.229  -1.731   0.022   0.359   0.619
E T  2WNS.A.1              99    0.459  63.663  -0.194   0.021   0.451   0.528
E K  2WNS.A.1             100    0.449  92.400  -0.525   0.021   0.451   0.528
E R  2WNS.A.1             101    0.379  86.699   0.195   0.023   0.655   0.322
B L  2WNS.A.1             102    0.299  54.802  -0.403   0.018   0.846   0.136
B V  2WNS.A.1             103    0.276  42.452  -0.197   0.018   0.846   0.136
E E  2WNS.A.1             104    0.462  80.676  -0.505   0.021   0.756   0.223
E G  2WNS.A.1             105    0.366  28.788  -1.166   0.022   0.552   0.426
E T  2WNS.A.1             106    0.448  62.110  -0.623   0.022   0.359   0.619
B I  2WNS.A.1             107    0.186  34.392  -0.535   0.020   0.205   0.775
E N  2WNS.A.1             108    0.488  71.458   0.676   0.018   0.088   0.893
E P  2WNS.A.1             109    0.663  94.136   0.880   0.018   0.019   0.964
E G  2WNS.A.1             110    0.579  45.599  -0.767   0.003   0.003   0.994
E E  2WNS.A.1             111    0.357  62.350   1.696   0.005   0.045   0.951
E T  2WNS.A.1             112    0.322  44.620   1.838   0.004   0.616   0.381
B C  2WNS.A.1             113    0.023   3.271   1.424   0.001   0.900   0.099
B L  2WNS.A.1             114    0.024   4.321   1.613   0.006   0.962   0.032
B I  2WNS.A.1             115    0.030   5.642   1.224   0.006   0.962   0.032
B I  2WNS.A.1             116    0.026   4.755   1.277   0.011   0.918   0.071
B E  2WNS.A.1             117    0.075  13.033   0.441   0.169   0.612   0.219
B D  2WNS.A.1             118    0.090  12.926  -0.382   0.352   0.332   0.316
B V  2WNS.A.1             119    0.074  11.328   0.571   0.478   0.309   0.214
B V  2WNS.A.1             120    0.081  12.404   0.647   0.538   0.173   0.289
E T  2WNS.A.1             121    0.308  42.761   0.104   0.455   0.046   0.498
B S  2WNS.A.1             122    0.216  25.315   0.268   0.181   0.016   0.803
B G  2WNS.A.1             123    0.178  14.009  -1.613   0.406   0.004   0.590
E S  2WNS.A.1             124    0.357  41.899   0.250   0.858   0.002   0.139
B S  2WNS.A.1             125    0.127  14.931   0.355   0.970   0.001   0.030
B V  2WNS.A.1             126    0.033   5.103   0.136   0.970   0.001   0.030
E L  2WNS.A.1             127    0.300  54.930   1.469   0.988   0.000   0.012
E E  2WNS.A.1             128    0.280  48.864   1.413   0.970   0.001   0.030
B T  2WNS.A.1             129    0.016   2.247   1.090   0.970   0.001   0.030
B V  2WNS.A.1             130    0.067  10.298   0.451   0.970   0.001   0.030
E E  2WNS.A.1             131    0.531  92.766   2.086   0.988   0.000   0.012
B V  2WNS.A.1             132    0.091  14.033   1.432   0.988   0.000   0.012
B L  2WNS.A.1             133    0.018   3.351   1.132   0.970   0.001   0.030
E Q  2WNS.A.1             134    0.532  94.997   1.970   0.970   0.001   0.030
E K  2WNS.A.1             135    0.738 151.807   1.738   0.858   0.002   0.139
B E  2WNS.A.1             136    0.224  39.115   1.166   0.246   0.004   0.750
E G  2WNS.A.1             137    0.737  58.010   0.770   0.003   0.003   0.994
B L  2WNS.A.1             138    0.074  13.604  -0.358   0.005   0.015   0.979
E K  2WNS.A.1             139    0.548 112.682   1.950   0.004   0.514   0.481
B V  2WNS.A.1             140    0.136  20.872   1.493   0.001   0.959   0.040
B T  2WNS.A.1             141    0.170  23.634   1.173   0.001   0.959   0.040
B D  2WNS.A.1             142    0.118  16.989   0.828   0.001   0.959   0.040
B A  2WNS.A.1             143    0.026   2.821   0.855   0.000   0.983   0.017
B I  2WNS.A.1             144    0.025   4.588   0.960   0.000   0.983   0.017
B V  2WNS.A.1             145    0.020   3.074   1.494   0.000   0.983   0.017
B L  2WNS.A.1             146    0.023   4.266   1.283   0.000   0.983   0.017
B L  2WNS.A.1             147    0.030   5.401   0.830   0.001   0.959   0.040
B D  2WNS.A.1             148    0.125  17.940   0.293   0.002   0.816   0.182
E R  2WNS.A.1             149    0.251  57.548   1.003   0.004   0.197   0.799
E E  2WNS.A.1             150    0.440  76.938  -0.160   0.018   0.047   0.935
E Q  2WNS.A.1             151    0.521  92.979   0.330   0.058   0.017   0.925
E G  2WNS.A.1             152    0.600  47.228  -0.105   0.115   0.016   0.868
B G  2WNS.A.1             153    0.107   8.421  -0.968   0.522   0.016   0.462
E K  2WNS.A.1             154    0.451  92.771   1.183   0.717   0.014   0.269
E D  2WNS.A.1             155    0.631  90.927   1.359   0.802   0.014   0.185
E K  2WNS.A.1             156    0.266  54.716   1.505   0.802   0.014   0.185
B L  2WNS.A.1             157    0.084  15.307   0.078   0.802   0.014   0.185
E Q  2WNS.A.1             158    0.668 119.216   1.422   0.802   0.014   0.185
E A  2WNS.A.1             159    0.746  82.264   0.879   0.600   0.003   0.397
E H  2WNS.A.1             160    0.409  74.379   0.821   0.176   0.004   0.820
E G  2WNS.A.1             161    0.785  61.787   0.218   0.003   0.003   0.994
B I  2WNS.A.1             162    0.076  14.079   0.879   0.005   0.045   0.951
E R  2WNS.A.1             163    0.452 103.508   1.409   0.005   0.262   0.733
B L  2WNS.A.1             164    0.065  11.828   0.672   0.021   0.756   0.223
B H  2WNS.A.1             165    0.243  44.238   1.455   0.011   0.918   0.071
B S  2WNS.A.1             166    0.068   7.958   0.001   0.011   0.918   0.071
B V  2WNS.A.1             167    0.048   7.439  -0.173   0.018   0.846   0.136
B C  2WNS.A.1             168    0.058   8.087   0.981   0.021   0.756   0.223
E T  2WNS.A.1             169    0.346  47.949   1.675   0.003   0.718   0.279
B L  2WNS.A.1             170    0.056  10.217   1.000   0.453   0.248   0.299
E S  2WNS.A.1             171    0.522  61.237   0.956   0.717   0.014   0.269
E K  2WNS.A.1             172    0.405  83.391   1.778   0.717   0.014   0.269
B M  2WNS.A.1             173    0.033   6.563   0.438   0.879   0.010   0.111
B L  2WNS.A.1             174    0.121  22.064   1.180   0.938   0.007   0.055
E E  2WNS.A.1             175    0.580 101.291   1.704   0.970   0.001   0.030
B I  2WNS.A.1             176    0.170  31.505   1.032   0.970   0.001   0.030
B L  2WNS.A.1             177    0.036   6.592  -0.837   0.970   0.001   0.030
E E  2WNS.A.1             178    0.536  93.692   1.427   0.923   0.002   0.076
E Q  2WNS.A.1             179    0.856 152.882   1.365   0.858   0.002   0.139
E Q  2WNS.A.1             180    0.457  81.674   1.388   0.246   0.004   0.750
E K  2WNS.A.1             181    0.602 123.790  -0.107   0.016   0.005   0.979
E K  2WNS.A.1             182    0.545 112.086   1.328   0.018   0.019   0.964
B V  2WNS.A.1             183    0.074  11.374  -0.259   0.018   0.019   0.964
E D  2WNS.A.1             184    0.447  64.384   1.394   0.018   0.019   0.964
E A  2WNS.A.1             185    0.691  76.192   1.387   0.923   0.002   0.076
E E  2WNS.A.1             186    0.729 127.409   1.262   0.858   0.002   0.139
B T  2WNS.A.1             187    0.219  30.389   0.792   0.858   0.002   0.139
B V  2WNS.A.1             188    0.121  18.659   1.241   0.970   0.001   0.030
E G  2WNS.A.1             189    0.669  52.682   1.838   0.970   0.001   0.030
E R  2WNS.A.1             190    0.345  79.074   2.359   0.970   0.001   0.030
B V  2WNS.A.1             191    0.029   4.457   0.484   0.970   0.001   0.030
E K  2WNS.A.1             192    0.443  91.146   1.977   0.970   0.001   0.030
E R  2WNS.A.1             193    0.566 129.568   2.122   0.923   0.002   0.076
B F  2WNS.A.1             194    0.132  26.472   0.674   0.923   0.002   0.076
E I  2WNS.A.1             195    0.339  62.807   0.927   0.782   0.003   0.216
E Q  2WNS.A.1             196    0.776 138.540   1.328   0.502   0.002   0.495
E E  2WNS.A.1             197    0.931 162.576   1.532   0.016   0.005   0.979

Article abstract

REFERENCE

A generic method for assignment of reliability scores applied to solvent accessibility predictions.
Bent Petersen, Thomas Nordahl Petersen, Pernille Andersen, Morten Nielsen and Claus Lundegaard¹.
BMC Structural Biology 2009, 9:51 doi:10.1186/1472-6807-9-51.

¹to whom correspondence should be addressed, e-mail: lunde@cbs.dtu.dk

Center for Biological Sequence Analysis, CBS, Department of Systems Biology.
The Technical University of Denmark, DK-2800 Lyngby, Denmark.

ABSTRACT

Background

Estimation of the reliability of specific real value predictions is nontrivial and the efficacy of this is often questionable. It is important to know if you can trust a given prediction and therefore the best methods associate a prediction with a reliability score or index. For discrete qualitative predictions, the reliability is conventionally estimated as the difference between output scores of selected classes. Such an approach is not feasible for methods that predict a biological feature as a single real value rather than a classification. As a solution to this challenge, we have implemented a method that predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score.

Results

An ensemble of artificial neural networks has been trained on a set of experimentally solved protein structures to predict the relative exposure of the amino acids. The method assigns a reliability score to each surface accessibility prediction as an inherent part of the training process. This is in contrast to the most commonly used procedures where reliabilities are obtained by post-processing the output.

Conclusion

The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20% of predictions sorted according to reliability. For this subset, values of 0.79 and 0.74 are obtained using our and the compared method, respectively. This tendency is true for any selected subset.

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Protein secondary structure and relative solvent accessibility

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Article abstract

REFERENCE

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