
PFRMAT AL
TARGET T0100
AUTHOR 1484-7979-5218
REMARK Weak signal from local threading and local sequence alignments
REMARK Local threading alignment used as a model
METHOD
METHOD  The results reported here are obtained using threading approach
METHOD  to the protein recognition problem. "Threading" is a fold
METHOD  recognition technique
METHOD  to match a sequence with a protein shape and plausible function.

METHOD  There are two essential components to threading:
METHOD  (a) finding an optimal alignment (with gaps) of a sequence into
METHOD      a structure
METHOD  (b) scoring different alignments and deciding on the best
METHOD      matching shape.
METHOD  Addressing both components we proposed new solutions to these
METHOD  problems.
METHOD
METHOD  To design score (energy) functions we use linear programming
METHOD  tools. In particular, a new model blending the higher
METHOD  prediction capacity of pairwise models with efficiency of
METHOD  profile potential is optimized.
METHOD
METHOD  We call it THreading Onion Model 2 (THOM2), since it employs
METHOD  the first and the second contact shell to characterize the
METHOD  structural environment of a given site.
METHOD  THOM2 model mimics effective pairwise interaction and
METHOD  incorporates significant cooperativity (N-body) effects.
METHOD  Linear programming is also used to determine optimal energy
METHOD  parameters for gaps. The new model provides an efficient and
METHOD  accurate threading approach, that can be used for genomics
METHOD  annotations.
METHOD
METHOD  The results are generated automatically (see LOOPP server
METHOD  http://ser-loopp.tc.cornell.edu/loopp.html) and include
METHOD  the best global and local threading (sequence to structure)
METHOD  alignments, as well as (structurally biased) local sequence
METHOD  to sequence alignments. The best matches according to a
METHOD  consensus score are reported as well.
METHOD
METHOD  First, matching of the whole query sequence(s) into whole
METHOD  structures, included in the library of folds, is evaluated
METHOD  using global variant of the dynamic programming algorithm
METHOD  and the novel THOM2 threading potential.
METHOD  Next, the same THOM2 potential and a local variant of the
METHOD  dynamic programming algorithm are used to evaluate
METHOD  compatibility between best matching fragments of the query
METHOD  sequence(s) and library structures.
METHOD  Finally, the best local sequence to sequence alignments
METHOD  are found using BLOSUM50 substitution matrix in conjunction
METHOD  with a gap penalty defined by a structural environment
METHOD  (number of neighbors) at a given site.
METHOD
METHOD  Our primary goal is to assign plausible structures to
METHOD  sequences that do not resemble significant sequence
METHOD  similarity to structurally (and functionally) chracterized
METHOD  proteins. To that end our primary predictions are based on
METHOD  threading and are complementary to standard sequence
METHOD  searches like BLAST or FASTA.
METHOD  Accordingly, the contributions of the global and local
METHOD  threading alignments to the consensus scores outweigh
METHOD  contributions of the sequence alignments.
METHOD  However, especially when there is no sufficiently similar
METHOD  structure in the fold library, a marginal
METHOD  sequence similarity can be used to enhance the confidence
METHOD  of predictions.
METHOD
METHOD  For details, please see http://www.tc.cornell.edu/CBIO/loopp/.
METHOD  Reference:  J. Meller and R. Elber, "The design of an
METHOD  efficient and accurate threading algorithm: Choice of energies
METHOD  and statistical verifications", Proteins, submitted.
METHOD
MODEL 1
PARENT 2sil
I   45        T   68
A   46        A   69
D   47        A   70
A   48        A   71
I   49        R   72
A   50        S   73
S   51        T   74
A   52        D   75
P   53        G   76
A   54        G   77
G   55        K   78
S   56        T   79
T   57        W   80
P   58        N   81
F   59        K   82
V   60        K   83
I   61        I   84
L   62        A   85
I   63        I   86
K   64        Y   87
N   65        N   88
G   66        D   89
V   67        R   90
Y   68        V   91
N   69        N   92
E   70        S   93
R   71        L   95
L   72        S   96
T   73        R   97
I   74        V   98
T   75        M   99
R   76        D   100
N   77        P   101
N   78        T   102
L   79        C   103
H   80        I   104
L   81        V   105
K   82        A   106
G   83        N   107
E   84        I   108
S   85        G   110
R   86        R   111
N   87        E   112
G   88        T   113
A   89        I   114
V   90        L   115
I   91        V   116
A   92        M   117
A   93        V   118
A   94        G   119
T   95        K   120
A   96        W   121
A   97        N   122
G   98        N   123
T   99        N   124
L   100       D   125
K   101       K   126
S   102       T   127
D   103       W   128
G   104       G   129
S   105       A   130
K   106       Y   131
W   107       R   132
G   108       D   133
T   109       K   134
A   110       A   135
G   111       P   136
S   112       D   137
S   113       T   138
T   114       D   139
I   115       W   140
T   116       D   141
I   117       L   142
S   118       V   143
A   119       L   144
K   120       Y   145
D   121       K   146
F   122       S   147
S   123       T    148
A   124        D   149
Q   125        D   150
S   126        G   151
L   127        V   152
T   128        T   153
I   129        F   154
R   130        S   155
N   131        K   156
D   132        V   157
F   133        E   158
D   134        T   159
F   135        N   160
P   136        I   161
A   137        H   162
N   138        D  163
Q   139       I   164
A   140       V   165
K   141       T   166
S   142       K   167
D   143       N   168
S   144       G   169
D   145       T   170
S   146       I   171
S   147       S   172
K   148       A   173
I   149       M   174
K   150       L   175
D   151       G   176
T   152       G   177
Q   153       V   178
A   154       G   179
V   155       S   180
A   156       G   181
L   157       L   182
Y   158       Q   183
V   159       L   184
T   160       N   185
K   161       D   186
G    163      G   187
D    164      K   188
R    165      L   189
A    166      V   190
Y    167      F   191
F    168      P   192
K    169      V   193
D    170      Q   194
V    171      M   195
S    172      V   196
L    173      R   197
V    174      T   198
G    175      K   199
Y    176      N   200
Q    177      I   201
D    178      T   203
T    179      V   204
L    180      L   205
Y    181      N   206
V    182      T   207
S    183      S   208
G    184      F   209
G    185      I   210
R    186      Y   211
S    187      S   212
F    188      T   213
F    189      G   215
S    190      I   216
D    191      T   217
C    192      W   218
R    193      S   219
I    194      L   220
S    195      P   221
G    196      S   222
T    197      G   223
V    198      Y   224
D    199      C   225
F    200      G   227
I    201      F   228
F    202      G   229
G    203      S   230
D    204      E   231
G    205      N   232
T    206      N   233
A    207      I   234
L    208      I   235
F    209      E   236
N    210      F   237
N    211      S   240
C    212      L   241
D    213      V   242
L    214      N   243
V    215      N   244
S    216      I   245
R    217      R   246
Y    218      N   247
R    219      S   248
A    220      G   249
D    221      L   250
V    222      R   251
K    223      R   252
S    224      S   253
G    225      F   254
N    226      E   255
V    227      T   256
S    228      K   257
G    229      D   258
Y    230      F   259
L    231      G   260
T    232      K   261
A    233      T   262
P    234      W   263
S    235      T   264
T    236      E   265
N    237      F   266
I    238      P   267
N    239      P   268
Q    240      M   269
K    241      D   270
Y    242      K   271
G    243      K   272
L    244      V   273
V    245      D   274
I    246      N   275
T    247      R   276
N    248      N   277
S    249      H   278
R    250      G   279
V    251      V   280
I    252      Q   281
R    253      G   282
E    254      S   283
S    255      T   284
D    256      I   285
S    257      T   286
V    258      I   287
P    259      P   288
A    260      S   289
K    261      G   290
S    262      N   291
Y    263      K   292
G    264      L   293
L    265      V   294
TER
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