

PFRMAT ABF1
TARGET T0038
AUTHOR 6094-1771-1985 
AUTHOR Lihua Yu, Chrysanthe G. Gaitatzes, James V. White, Temple F. Smith
AUTHOR Boston University
AUTHOR tsmith@darwin.bu.edu
REMARK
REMARK Method description:
REMARK
REMARK We are predicting the protein structures from primary sequences
REMARK in the following way.
REMARK 
REMARK We use discrete state space models (DSMs) [ref. 1,2,3] to compute the
REMARK probabilities that the protein belongs to each of four distinct classes 
REMARK (alpha, beta, alpha-beta, irregular). If one of the classes has a probability 
REMARK greater than 0.8, then (1) we compute probabilities that the protein belongs to 
REMARK each of distinct structure classes (e.g. beta-propeller, four-alpha-helix 
REMARK bundle, alpha-beta-8-barrel...), and (2) we use a smoothing algorithm to predict 
REMARK the secondary structure [ref. 4]. The smoothing algorithm computes the 
REMARK probabilities that each amino acid is in either a helix, a strand, a turn, 
REMARK or a coil. 
REMARK
REMARK The three dimensional structure is predicted by generalized homologous 
REMARK extension modelling. Since there is no sequence homologue in 
REMARK Brookhaven database for the given protein, we selected a structure analog, 
REMARK based on the predicted structure class and secondary structures. Using 
REMARK QUANTA version 4.1 (copyright MSI Inc.), we mutated the amino acids of the 
REMARK structure analog into those of the given sequence. We then used CHARMm 
REMARK version 23.1 [ref.5] to refine the three dimensional structure of the core 
REMARK segments by energy minimization.
REMARK
REMARK References
REMARK 1. White, J.V., Stultz, C.M., Smith, T.F. (1994) Protein classification by 
REMARK stochastic modelling and optimal filtering of amino-acid sequences. 
REMARK Mathematical Biosciences 119:35-75.
REMARK 2. Stultz, C.M., Nambudripad, R., Lathrop, R.H., & White, J.V.  
REMARK Predicting protein structure with probabilistic models. In press.
REMARK 3. World wide web URL: http://bmerc-www.bu.edu/psa/
REMARK 4.Stultz, C.M., White, J.V., & Smith, T.F. (1993). Structure analysis based on
REMARK state-space modelling. Protein Science 2:305-314.
REMARK 5. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., Sates, D.J., Swaminathan, 
REMARK S., and Karplus, M. (1993) J. Comput. Chem., 4, 187-217.
REMARK 
REMARK In the following prediction, the coil segments being predicted as tight turns by
REMARK our method are indicated by a comment following the line.
REMARK
BEGDAT 1.1  1  0.9681
SS 152
A        C        1    
S        C        0.987
P        C        0.973
I        C        0.922
G        C        0.887
E        C        0.812
G        C        0.762
T        C        0.631
F        C        0.587
D        C        0.705
D        C        0.846
G        C        0.913
P        C        0.915		#turn
E        C        0.785		#turn
G        C        0.64 		#turn
W        E        0.659
V        E        0.829
A        E        0.816
Y        E        0.759
G        E        0.555
T        C        0.562
D        C        0.649
G        C        0.719
P        C        0.648
L        C        0.495
D        C        0.491
T        E        0.502
S        C        0.541
T        C        0.55 
G        C        0.556
A        E        0.512
L        E        0.711
C        E        0.786
V        E        0.872
A        E        0.854
V        E        0.764
P        C        0.679		#turn
A        C        0.733		#turn
G        C        0.808		#turn
S        C        0.753		#turn
A        E        0.614
Q        E        0.609
Y        E        0.708
G        E        0.693
V        E        0.721
G        E        0.787
V        E        0.832
V        E        0.78 
L        E        0.571
N        C        0.531
G        C        0.503
V        E        0.659
A        E        0.807
I        E        0.758
E        C        0.651		#turn
E        C        0.794		#turn
G        C        0.849		#turn
T        C        0.772		#turn
T        E        0.655
Y        E        0.797
T        E        0.855
L        E        0.883
R        E        0.879
Y        E        0.847
T        E        0.785
A        E        0.662
T        E        0.508
A        C        0.72 
S        C        0.833		#turn
T        C        0.733		#turn
D        C        0.549
V        E        0.743
T        E        0.894
V        E        0.922
R        E        0.917
A        E        0.897
L        E        0.854
V        E        0.802
G        C        0.52 
Q        C        0.872		#turn
N        C        0.884		#turn
G        C        0.872		#turn
A        C        0.664
P        E        0.575
Y        E        0.663
G        E        0.698
T        E        0.72 
V        E        0.729
L        E        0.663
D        E        0.502
T        C        0.595
S        C        0.675
P        C        0.652
A        E        0.515
L        E        0.695
T        E        0.737
S        E        0.708
E        C        0.725		#turn
P        C        0.855		#turn
R        C        0.836		#turn
Q        C        0.83 		#turn
V        E        0.628
T        E        0.727
E        E        0.72 
T        E        0.754
F        E        0.768
T        E        0.707
A        E        0.625
S        E        0.535
A        C        0.505
T        C        0.606
Y        C        0.63 
P        C        0.632
A        C        0.583
T        C        0.563
P        C        0.562
A        E        0.41 
A        E        0.406
D        C        0.59 
D        C        0.731
P        C        0.89 		#turn
E        C        0.821		#turn
G        C        0.758		#turn
Q        C        0.562
I        E        0.814
A        E        0.842
F        E        0.84 
Q        E        0.689
L        E        0.603
G        C        0.505
G        C        0.566
F        E        0.509
S        C        0.63 
A        C        0.627
D        C        0.601
A        E        0.488
W        E        0.747
T        E        0.786
L        E        0.775
C        E        0.687
L        C        0.561
D        C        0.708
D        C        0.704
V        C        0.575
A        E        0.601
L        E        0.66 
D        E        0.608
S        E        0.632
E        E        0.692
V        E        0.74 
E        E        0.741
L        E        0.674
ENDDAT 1.1
END
