SSENVID - assignment protein secondary structure and environment

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Fri Dec 14 05:27:40 EST 2001


SSENVID - Program for assignment protein secondary structure and environment 
assignment from atomic coordinates.
           http://www.softberry.com/cgi-bin/ssenvid.pl
SSENVID is a program to recognize secondary structural elements in proteins 
from their atomic coordinates. It analyzes both hydrogen bond and mainchain 
dihedral angles, as well some probabilistic measures. SSENVID also computes 
accessible surface area, polarity and environment classes. SSENVID's unique 
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. You can try it here.

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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

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