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Protein secondary structure and environment assignment from atomic coordinates

SSENVID is a program to recognize secondary structural elements in proteins from their atomic coordinates. It performs the same task as DSSP by Kabsch and Sander (1983) or STRIDE by Frishman & Argos (1995) with analyzing both hydrogen bond and mainchain dihedral angles, as well some probabilistic measures. SSENVID also computes accessible surface area, polarity and environment classes as defined by Bowie, Luthy, Eisenberg (1991). SSENVID's new feature is the probability (quality) of secondary structure assignment for each amino acids.

SSENVID computes 3D protein characteristics which are used in structure prediction by measuring the compatibility between protein sequences and known protein structures.

SSENVID output:

  SSENVID - Protein secondary structure and environment assignment
             from atomic coordinates (Softberry Inc., 2001)

  Ch   - Chain
  ResN - PDB resnumber
  Nam  - Amino acid sequence in three letter code
  Ab   - Area Buried
  Fp   - Fraction Polar
  SS   - Secondary structure assignment (E-beta sheet, H,G,I-helices, T-turn)
  PDBSS- Original PDB secondary structure assignment (if provided)
  Env  - Side-Chain Environment Class
  PrHel- Probability of helix
  PrBet- Probability of beta bridge

     ResN  Nam   Ab     Fp   SS  PDBSS  Env   PrHel  PrBet

  A     1  VAL   79.1   0.35  C    C   P1      0.00    0.00
  A     2  ALA   26.2   0.60  C    C   E       0.00    0.09
  A     3  ILE  157.0   0.23  E    C   B1      0.13    0.88
  A     4  LYS  105.5   0.72  E    C   P2      0.13    0.88
  A     5  MET  172.0   0.30  E    C   B1      0.13    0.88
  A     6  GLY   40.0   0.37  C    C   E       0.13    0.16
  A     7  ALA   64.5   0.47  C    C   P1      0.13    0.00
  A     8  ASP   54.5   0.77  T    C   P2      0.08    0.00
  A     9  ASN   36.7   0.57  T    C   E       0.08    0.00
  A    10  GLY   14.0   0.53  C    C   E       0.07    0.00
  A    11  MET   33.1   0.80  C    C   E       0.13    0.00
  A    12  LEU   97.5   0.49  C    C   P1      0.13    0.01
  A    13  ALA   53.7   0.47  C    C   P1      0.13    0.07
  A    14  PHE  188.1   0.34  C    C   B2      0.13    0.88
  A    15  GLU   96.0   0.54  C    C   P1      0.13    0.88
  A    16  PRO   66.5   0.56  C    C   P1      0.13    0.00
  A    17  SER   34.9   0.81  C    C   E       0.13    0.00
  A    18  THR   57.7   0.63  E    E   P2      0.13    0.86
  A    19  ILE  139.9   0.29  E    E   B1      0.13    0.86
  A    20  GLU   87.9   0.51  E    E   P1      0.13    0.88
  A    21  ILE  157.0   0.35  E    E   B2      0.13    0.88
  A    22  GLN   45.2   0.80  C    E   P2      0.16    0.00
  A    23  ALA   47.2   0.56  T    C   P1      0.16    0.16
  A    24  GLY   21.5   0.61  T    C   E       0.16    0.00
  A    25  ASP   70.7   0.46  C    C   P1      0.16    0.30
  A    26  THR   63.0   0.71  E    E   P2      0.13    0.88
  A    27  VAL  129.9   0.24  E    E   B1      0.13    0.88
  A    28  GLN   95.7   0.50  E    E   P1      0.13    0.88
  A    29  TRP  234.0   0.16  E    E   B1      0.13    0.90
  A    30  VAL  112.0   0.42  E    E   P1      0.13    0.90
  A    31  ASN  122.7   0.41  E    E   B2      0.26    0.88
  A    32  ASN   90.0   0.54  C    C   P1      0.26    0.00
  A    33  LYS   91.2   0.71  C    C   P2      0.26    0.01
  A    34  LEU   38.7   0.66  C    C   E       0.13    0.00
  A    35  ALA   56.4   0.64  C    C   P2      0.13    0.01
  A    36  PRO   70.4   0.47  C    C   P1      0.13    0.00
  A    37  HIS  175.0   0.30  E    C   B1      0.13    0.90
  A    38  ASN  117.8   0.37  E    C   B2      0.13    0.17
  A    39  VAL  130.0   0.18  E    C   B1      0.13    0.88
  A    40  VAL  111.6   0.48  E    C   P1      0.13    0.87
  A    41  VAL  129.2   0.24  E    C   B1      0.13    0.87
  A    42  GLU   51.1   0.68  T    C   P2      0.08    0.17
  A    49  GLY    0.0   0.77  T    C   E       0.08    0.09
  A    52  GLN  104.9   0.50  C    C   P1      0.22    0.30
  A    53  PRO    0.0   0.86  G    H   E       0.96    0.00
  A    54  GLU   50.1   0.69  G    H   P2      0.96    0.00
  A    55  LEU  144.4   0.34  G    H   B2      0.96    0.00
  A    56  SER   81.2   0.40  C    C   P1      0.07    0.00
  A    57  HIS  111.3   0.53  E    C   P1      0.13    0.88
  A    58  LYS   10.1   0.81  E    C   E       0.13    0.00
  A    59  ASP    0.0   0.82  E    C   E       0.13    0.00
  A    62  LEU   83.4   0.49  E    C   P1      0.13    0.17
  A    63  ALA   70.5   0.46  E    C   P1      0.26    0.90
  A    64  PHE   20.5   0.67  C    C   E       0.26    0.01
  A    65  SER   22.2   0.74  C    C   E       0.26    0.00
  A    66  PRO   10.6   0.83  T    C   E       0.34    0.17
  A    67  GLY   21.1   0.56  T    C   E       0.34    0.00
  A    68  GLU  102.2   0.56  C    C   P1      0.34    0.09
  A    69  THR   73.7   0.54  E    E   P1      0.13    0.90
  A    70  PHE  165.9   0.41  E    E   B2      0.13    0.90
  A    71  GLU   83.4   0.56  E    E   P1      0.13    0.88
  A    72  ALA   58.9   0.46  E    E   P1      0.13    0.88
  A    73  THR   57.1   0.67  E    E   P2      0.13    0.88
  A    74  PHE  188.9   0.22  C    C   B1      0.13    0.30
  A    75  SER   27.9   0.59  C    C   E       0.13    0.00
  A    76  GLU    0.0   0.86  C    C   E       0.13    0.00
 .......
 
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