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Article #196SSENVID - assignment protein secondary structure and environment
From: webmaster_softberry_com
Date: Fri, 14 Dec 2001 10:28
Date: Fri, 14 Dec 2001 10:28
59 lines
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5132 bytes
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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