Fold Recognition using Contact Information of Residue Pairs



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Abstract:

First statistical contact potential (SCP): Statistical potential derived by the maximization of the perceptron criterion

Reference: Vendruscolo M, Domany E, Pairwise contact potentials are unsuitable for protein folding, J Chem Phys 109:11101–11108, 1998.

  A R N D C Q E G H I L K M F P S T W Y V
A -0.02808                                      
R .01438 .0543                                    
N .09084 -0.0321 -0.07726                                  
D 0.01673 -0.1196 .07582 .08769                                
C .00069 .1005 .00943 .01585 -0.18164                              
Q .02297 -0.1314 .04386 -0.08755 .03575 .0197                            
E .09398 -0.1873 -0.0072 -0.00952 .02004 -0.0372 .0865                          
G .00253 .0711 -0.03475 -0.06461 -0.01841 .02 .086 -0.1748                        
H .00916 -0.0218 -0.00094 -0.0338 -0.03699 .0522 -0.1188 .0876 -0.02649                      
I -0.10044 .0338 .04248 .01813 -0.00256 .0548 .05 .0339 -0.00602 -0.0449                    
L -0.00789 .0164 .01271 .02074 .07471 .0215 .0173 .0932 .01358 -0.1608 -0.098                  
K .04718 .0131 .00884 -0.09309 .01137 -0.0489 -0.1536 .0376 .02636 .0175 .0509 .1122                
M .07572 .0583 .03734 .06106 .13069 .0304 .1327 .0944 -0.01512 -0.0974 -0.0624 .0602 .014              
F .03878 .0041 .00294 .01164 -0.0452 -0.1336 .0136 -0.1882 -0.09404 -0.116 -0.0551 .0384 -0.0876 -0.11542            
P .07816 -0.062 .01251 .04375 -0.01505 -0.0837 .0724 .0982 -0.0737 .0427 .0211 0.1598 -0.0395 .06601 .013          
S .00648 .0856 -0.00054 .00055 .01582 -0.0284 -0.1229 -0.0505 .00167 .007 .0255 -0.0366 .0551 -0.00013 .112 -0.0667        
T -0.03831 -0.093 .00302 -0.0422 .14216 .0725 .0788 -0.0574 -0.00499 .0158 .0169 .0082 .0894 .01352 .062 .00262 .06636      
W .0095 -0.0219 -0.01788 -0.00609 .04886 -0.0157 .1134 .1083 -0.01956 .0093 -0.041 .0117 -0.2448 .00303 -0.174 .07002 .06563 -0.0382    
Y 0.01587 -0.0652 -0.07248 .00165 .02167 -0.029 -0.0183 0.0607 -0.07678 -0.0112 0.054 -0.109 0.0085 0.01074 -0.091 0.06797 0.05679 0.061 -0.0484  
V -0.08515 0.023 0.01472 0.0684 -0.06069 0.0097 0.0595 0.0406 -0.001 -0.1095 -0.1274 0.0331 -0.0634 -0.03358 0.027 0.03116 -0.00024 0.0260 -0.0303 -0.07182
 

Second SCP: Statistical contact potential derived from 25 x-ray protein structures
Reference: Tanaka S, Scheraga HA, Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins, Macromolecules 9:945–950, 1976.

  A R N D C Q E G H I L K M F P S T W Y V
A -2.6                                      
R -3.4 -4.3                                    
N -3.1 -4.1 -3.2                                  
D -2.8 -3.9 -3.1 -2.7                                
C -4.2 -5.3 -4.9 -4.2 -7.1                              
Q -3.5 -4.5 -3.8 -3.2 -5 -3.4                            
E -3.0 -4.2 -3.4 -3.3 -4.4 -3.6 -2.8                          
G -3.8 -4.5 -4 -3.7 -5.4 -4.4 -3.8 -3.9                        
H -4.0 -4.9 -4.4 -4.3 -5.6 -4.7 -4.5 -4.7 -4.9                      
I -5.9 -6.2 -5.8 -5.4 -7.3 -5.9 -5.7 -6.3 -6.6 -8.2                    
L -4.8 -5.1 -4.6 -4.3 -6.2 -5 -4.6 -5.2 -5.6 -7.5 -6                  
K -3.1 -3.6 -3.3 -3.2 -4.4 -3.7 -3.8 -3.8 -4.1 -5.6 -4.6 -2.7                
M -4.6 -5 -4.2 -4.3 -6.2 -3.5 -4.6 -5.1 -5.4 -7.4 -6.3 -4.7 -5.8              
F -5.1 -5.8 -5 -4.9 -6.8 -5.3 -5 -5.6 -6.4 -8 -7 -4.9 -6.6 -7.1            
P -3.4 -4.2 -3.6 -3.3 -5.3 -4 -3.5 -4.2 -4.5 -6 -4.8 -3.6 -5.1 -5.2 -3.5          
S -2.9 -3.8 -3.1 -2.7 -4.6 -3.6 -3.2 -3.8 -4.3 -5.5 -4.4 -3 -4.1 -4.7 -3.4 -2.5        
T -3.3 -4 -3.5 -3.1 -4.8 -3.7 -3.3 -4.1 -4.5 -5.9 -4.8 -3.3 -4.6 -5.1 -3.6 -3.3 -3.1      
W -5.2 -5.8 -5.3 -5.1 -6.9 -5.8 -5.2 -5.8 -6.5 -7.8 -6.8 -5 -6.9 -7.4 -5.6 -5 -5.1 -6.8    
Y -4.7 -5.6 -5 -4.7 -6.6 -5.2 -4.9 -5.4 -6.1 -7.4 -6.2 -4.9 -6.1 -6.6 -5.2 -4.7 -4.9 -6.8 -6  
V -4.3 -4.9 -4.3 -4 -6 -4.7 -4.2 -5.1 -5.3 -7.3 -6.2 -4.2 -6 -6.5 -4.7 -4.2 -4.4 -6.5 -5.9 -5.5

 

Third SCP: Mixed quasichemical and optimization-based protein contact potential
Reference: Thomas PD, Dill KA, An iterative method for extracting energy-like quantities from protein structures, Proc Natl Acad Sci USA 93:11628–11633, 1996.

  A R N D C Q E G H I L K M F P S T W Y V
A -0.08                                      
R 0.07  0.23                                    
N -0.14 0.04 -0.86                                  
D 0.1 -0.15 -0.12 0.6                                
C -0.3 -0.4 -0.32 0.55 -1.79                              
Q -0.11 0.62 -0.05 0.46 -0.49 -0.08                            
E 0.03 -0.26 -0.25 0.68 0.04 0.62 0.21                          
G -0.09 -0.15 -0.18 -0.06 -0.42 0.12 0.4 0.04                        
H -0.15 -0.01 0.06 -0.06 -0.82 0.05 -0.53 0 0.14                      
I -0.64  -0.08  0.39  0.04 -0.48 -0.39 -0.2 0.4  -0.52 -0.71                    
L -0.57 -0.1 -0.1 0.5 -0.69 -0.13 -0.05 -0.08  -0.36  -1.04 -1.14                  
K 0 0.3 0.18 -0.09 0 0.04 -0.09 0.1  0.14  -0.26 0.1 1.45                
M 0.05 -0.43  0.31  1.07  -1.23 -0.54 0.02 0  -0.35  -0.41 -0.31 0.55 0.36              
F -0.05 -0.22  -0.02 0.2  -0.98 0.1 0.19 0.21  -0.75  -0.66 -1.02 -0.17 -1.03 -0.61            
P 0.41 -0.02 0.11 0.84 0.07 -0.21 0.33 0.4 -0.22  0.25 0.09 0.51 -0.25 -0.43 0.28          
S -0.01 0.61 0.37 -0.09 -0.2 0.4 0.3 -0.04  -0.59  -0.13 -0.07 0.18 -0.47 0.14 0.44 -0.13        
T -0.22 -0.17 -0.27 -0.03 -0.38 -0.17 0.15 0.13  -0.27  -0.29 -0.39 0.09 0.06 -0.19 0.36 0.05 0.26      
W -0.08 -0.78 -0.68 0.24 -0.3 0.4 0.32 -0.14  -0.41  -0.89 -0.97 -0.3 -0.07 -0.89 -0.44 -0.2 0.07 0.02    
Y -0.37 0.21 -0.74 0.11 -0.96 -0.39 0.22  -0.32  -0.67 -0.87 -0.6 -0.2 -1.1 -0.82 -0.45 0.25 -0.23 -0.99 0.35  
V -0.60 -0.48 -0.24 0.25 -0.94 -0.09 -0.02  -0.2  -0.35  -0.98  -1.03 -0.08 -0.94 -0.78 -0.08 -0.31 0.06 -0.6 -0.7 -1.15


Fourth SCP: Distance-dependent statistical potential (contacts within 0-5 Angstrooms)

Reference: Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D, Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins, Proteins 34:82–95, 1999.

  A R N D C Q E G H I L K M F P S T W Y V
A -0.13571                                      
R 0.37121 0.23245                                    
N 0.25935 -0.2705 -0.61455                                  
D 0.33397 -0.78243 -0.4183 0.06704                                
C 0.23079 0.49103 0.32481 0.53024 -1.79243                              
Q 0.26575 -0.25307 -0.26143 -0.00061 0.252  -0.24068                            
E 0.26471 -0.78607 -0.1801 0.24572 0.6636  -0.05835 0.51101                          
G -0.01467 -0.08319 -0.37069 -0.22435 0.20423 -0.0189 0.14922 -0.48115                        
H 0.32413 -0.10894 -0.0042 -0.47402 0.24383 -0.03046  -0.10674 0.08603  -0.23317                      
I -0.22176 0.33584 0.38282 0.44972 0.12534 0.20555 0.21945 0.36527  0.10553 -0.317                    
L -0.15025 0.19784 0.35359 0.382 0.10747 0.07523  0.19892 0.30617 0.11443 -0.1261 -0.19983                  
K 0.39894 0.55155 -0.07038 -0.90014 0.73178  -0.24804 -0.92364 0.00501  0.00361 0.217 0.21292 0.56407                
M 0.03521 0.12999 0.02882 0.32317 0.04462  -0.03542 0.15161 0.14609 0.01416 -0.0879 -0.1286 0.15363 -0.13998              
F 0.08139 0.03136 0.26608 0.53784 0.09641 0.1434 0.25134 0.21293  0.03923 -0.1911 -0.22682 0.04828 -0.2336 -0.24651            
P 0.03615 -0.06999 -0.20175 -0.21449 -0.04477 -0.16569 -0.14194 -0.18438 -0.27877 0.5603 0.35217 0.04081 0.11287 -0.10484 -0.0417          
S 0.10475 -0.02548 -0.28825 -0.50285 0.11283  -0.0614 -0.35312 -0.27119 -0.11302 0.313 0.27135 0.02715 0.19696 .28005 -0.10791 -0.20955        
T -0.04679 -0.05313 -0.28531 -0.36579 0.27539  -0.23014 -0.29144 -0.24551 -0.25624 0.2867 0.31011 -0.13219 0.3009 .37472 .02844 -0.32381 -0.19546      
W 0.20001 -0.33116 0.28602 0.50378 0.09401 -0.0457 0.16071 0.24344 -0.17229 -0.1598 -0.16843 -0.24586 -0.09998 -0.13588 -0.55908 .36554 .33614 .05462    
Y 0.12835 -0.14488 0.12638 0.46473 0.16464  -0.03777 0.18883 0.1064 0.02691 -0.1696 -0.20609 -0.16896 -0.22924 -0.01526 -0.41613 .31614 .36576 -0.0328 -0.01669  
V -0.27134 0.33279 0.47451 0.44658 0.09778 0.08581 0.22764 0.23105 0.15787 -0.1963 -0.10641 0.23784 0.00637 -0.08226 .39761 .15369 .14755 .12174 .02059 -0.29733



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