Bioinformatics

Molecular biology in the internet

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Bioinformatics

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Sequence comparisons

Homology searches

Motif searches

Hidden Markov models

Hydrophobicity analyses

Topology and helix packing

Protein localization

Secondary structure

Super-secondary structure

3D structure

 

    Example of a secondary structure prediction using Prof:

    
    MODEL
    M   C    0.936
    I   C    0.715
    M   C    0.618
    T   C    0.533
    S   C    0.428
    M   C    0.419
    T   C    0.407
    L   C    0.444
    D   C    0.540
    L   C    0.642
    P   C    0.765
    R   C    0.748
    R   C    0.768
    F   C    0.822
    P   C    0.862
    W   C    0.842
    P   C    0.662
    T   E    0.477
    L   E    0.695
    L   E    0.812
    S   E    0.709
    V   E    0.621
    C   E    0.495
    I   C    0.436
    H   C    0.532
    G   H    0.628
    A   H    0.733
    V   H    0.823
    V   H    0.894
    A   H    0.883
    G   H    0.855
    L   H    0.789
    L   H    0.782
    Y   H    0.722
    T   H    0.578
    S   C    0.442
    V   C    0.418
    H   C    0.417
    Q   C    0.431
    V   E    0.453
    I   E    0.454
    E   C    0.616
    L   C    0.774
    P   C    0.864
    A   C    0.898
    P   C    0.903
    A   C    0.909
    Q   C    0.891
    P   C    0.789
    I   E    0.575
    S   E    0.843
    V   E    0.918
    T   E    0.914
    M   E    0.865
    V   E    0.658
    T   C    0.558
    P   C    0.719
    A   C    0.764
    D   C    0.698
    L   C    0.668
    E   C    0.640
    P   C    0.584
    P   C    0.621
    Q   C    0.596
    A   C    0.612
    V   C    0.577
    Q   C    0.568
    P   C    0.561
    P   C    0.534
    P   C    0.517
    E   C    0.510
    P   C    0.493
    V   C    0.470
    V   C    0.485
    E   C    0.527
    P   C    0.545
    E   C    0.542
    P   C    0.552
    E   C    0.559
    P   C    0.568
    E   C    0.576
    P   C    0.579
    I   C    0.584
    P   C    0.582
    E   C    0.577
    P   C    0.552
    P   C    0.523
    K   C    0.515
    E   C    0.479
    A   C    0.459
    P   C    0.408
    V   E    0.453
    V   E    0.513
    I   E    0.483
    E   E    0.415
    K   C    0.439
    P   C    0.483
    K   C    0.498
    P   C    0.533
    K   C    0.559
    P   C    0.597
    K   C    0.592
    P   C    0.596
    K   C    0.596
    P   C    0.606
    K   C    0.569
    P   C    0.564
    V   C    0.546
    K   C    0.572
    K   C    0.518
    V   C    0.451
    Q   C    0.487
    E   C    0.596
    Q   C    0.664
    P   C    0.751
    K   C    0.795
    R   C    0.805
    D   C    0.843
    V   C    0.895
    K   C    0.910
    P   C    0.898
    V   C    0.910
    E   C    0.924
    S   C    0.928
    R   C    0.920
    P   C    0.922
    A   C    0.924
    S   C    0.920
    P   C    0.913
    F   C    0.904
    E   C    0.900
    N   C    0.888
    T   C    0.875
    A   C    0.818
    P   C    0.714
    A   C    0.642
    R   C    0.592
    L   C    0.548
    T   C    0.539
    S   C    0.501
    S   C    0.449
    T   C    0.415
    A   C    0.393
    T   C    0.391
    A   C    0.385
    A   C    0.360
    T   C    0.375
    S   C    0.422
    K   C    0.498
    P   C    0.518
    V   C    0.464
    T   C    0.448
    S   C    0.475
    V   C    0.621
    A   C    0.734
    S   C    0.836
    G   C    0.863
    P   C    0.817
    R   C    0.688
    A   C    0.599
    L   C    0.574
    S   C    0.704
    R   C    0.870
    N   C    0.908
    Q   C    0.898
    P   C    0.881
    Q   C    0.861
    Y   C    0.872
    P   H    0.546
    A   H    0.777
    R   H    0.855
    A   H    0.911
    Q   H    0.927
    A   H    0.897
    L   H    0.746
    R   C    0.479
    I   C    0.747
    E   C    0.801
    G   C    0.635
    Q   E    0.789
    V   E    0.927
    K   E    0.954
    V   E    0.955
    K   E    0.948
    F   E    0.938
    D   E    0.920
    V   E    0.805
    T   E    0.511
    P   C    0.720
    D   C    0.849
    G   C    0.835
    R   C    0.801
    V   C    0.671
    D   C    0.516
    N   E    0.712
    V   E    0.892
    Q   E    0.936
    I   E    0.935
    L   E    0.862
    S   E    0.576
    A   C    0.692
    K   C    0.865
    P   C    0.869
    A   C    0.563
    N   H    0.587
    M   H    0.772
    F   H    0.845
    E   H    0.925
    R   H    0.948
    E   H    0.949
    V   H    0.950
    K   H    0.951
    N   H    0.948
    A   H    0.941
    M   H    0.943
    R   H    0.934
    R   H    0.906
    W   H    0.837
    R   H    0.727
    Y   H    0.553
    E   C    0.733
    P   C    0.885
    G   C    0.902
    K   C    0.880
    P   C    0.889
    G   C    0.888
    S   C    0.866
    G   C    0.748
    I   E    0.616
    V   E    0.866
    V   E    0.920
    N   E    0.942
    I   E    0.949
    L   E    0.935
    F   E    0.927
    K   E    0.840
    I   E    0.591
    N   C    0.615
    G   C    0.756
    T   C    0.715
    T   C    0.633
    E   C    0.650
    I   C    0.780
    Q   C    0.933
    END
    
    

 

Latest update of content: July 4, 2001


Ralf Koebnik
Institut de recherche pour le dèveloppement
UMR 5096, CNRS-UP-IRD
911, Avenue Agropolis, BP 64501
34394 Montpellier, Cedex 5
FRANCE
Phone: +33 (0)4 67 41 62 28
Fax: +33 (0)4 67 41 61 81
Email: koebnik(at)gmx.de
Please replace (at) by @.


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