workflow
0
0
497
388
206
210
212
206
210
212
255
255
255
191
204
212
191
204
212
206
210
212
206
210
212
255
255
255
191
204
212
191
204
212
206
210
212
206
210
212
191
204
212
191
204
212
191
204
212
Allosteric Pathway Computation Workflow
:/icons/application_form_edit.png
40
60
411
271
0
85
127
255
255
255
255
255
255
255
255
255
127
127
127
170
170
170
0
85
127
255
255
255
0
0
0
255
255
255
255
255
255
127
132
157
255
255
255
0
85
127
255
255
255
255
255
255
255
255
255
127
127
127
170
170
170
0
85
127
255
255
255
0
0
0
255
255
255
255
255
255
127
132
157
255
255
255
127
127
127
255
255
255
255
255
255
255
255
255
127
127
127
170
170
170
127
127
127
255
255
255
127
127
127
255
255
255
255
255
255
127
132
157
255
255
255
Qt::LeftToRight
false
QTabWidget::Triangular
2
Qt::ElideNone
Structure and Sequence
:/icons/brick_add.png
240
120
132
31
Enter Reference Sequence
Identifier in MSA
240
160
71
22
240
40
81
21
Select MSA File
40
210
91
21
Chain of Interest
140
212
55
22
QComboBox::AdjustToContentsOnFirstShow
310
210
75
24
background-color: #FFFFCC;
border-style: outset;
border-width: 2.1px;
border-radius: 10px;
border-color: white;
font: bold 10px;
color: gray;
min-width: 10em;
padding: 6px;
next
:/icons/control_end_blue.png
20
20
191
181
Reference Structure Selection
20
90
61
16
Qt::Horizontal
20
50
91
22
20
140
91
22
20
110
151
21
Input PDB Identifier (eg: 1KK7)
20
20
71
21
Select PDB file
90
90
21
16
OR
120
90
61
16
Qt::Horizontal
140
50
31
31
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;">Browse files for .pdb</p></body></html>
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"></p></body></html>
...
:/icons/folder_lightbulb.png
140
140
31
31
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;">Download file from RCSB</p></body></html>
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"></p></body></html>
...
:/icons/world_add.png
350
70
31
31
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;">Browse files for .aln </p></body></html>
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"></p></body></html>
...
:/icons/text_padding_left.png
240
70
91
22
Conservation
:/icons/chart_bar.png
220
210
75
24
background-color: #FFFFCC;
border-style: outset;
border-width: 2.1px;
border-radius: 10px;
border-color: white;
font: bold 10px;
color: gray;
min-width: 10em;
padding: 6px;
back
:/icons/control_start_blue.png
310
210
75
24
background-color: #FFFFCC;
border-style: outset;
border-width: 2.1px;
border-radius: 10px;
border-color: white;
font: bold 10px;
color: gray;
min-width: 10em;
padding: 6px;
next
:/icons/control_end_blue.png
60
20
281
131
Matrices for Conservation Weighting
200
30
24
24
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-size:10pt; color:#00ced1;">IDENTITY MATRIX</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#5f9ea0;"></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#696969;">Simplest matrix: a substitution score of one for a pair of matching amino acids and zero otherwise. </p></body></html>
QFrame::StyledPanel
QFrame::Raised
:/icons/tag_blue.png
false
2
200
60
24
24
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-size:10pt; color:#00ced1;">MIYATA MATRIX</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#5f9ea0;"></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#5f9ea0;"><span style=" color:#696969;">Reflects the idea that frequency of amino acid substitutions decreases linearly with increase of physical-chemical differences between the amino acid pair. Differences in both physical attribute (volume) and chemical attribute (polarity) are taken into consideration.</span></p></body></html>
QFrame::StyledPanel
QFrame::Raised
:/icons/tag_yellow.png
false
2
200
90
24
24
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-size:10pt; color:#00ced1;">WAC</span><span style=" font-size:10pt; color:#2f4f4f;"> </span><span style=" font-size:10pt; color:#00ced1;">(Wei-Altman-Chang) MATRIX</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#5f9ea0;"></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt; color:#696969;">Assigns substitution scores by examining physical-chemical and structural differences between environments of amino acid pairs.</p></body></html>
QFrame::StyledPanel
QFrame::Raised
:/icons/tag_green.png
false
2
60
30
81
19
Identity
60
60
81
19
Miyata
true
60
90
81
19
WAC
285
167
53
22
0
1000.000000000000000
0.000000000000000
1.000000000000000
60
160
202
42
131
135
135
131
135
135
127
127
127
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-weight:600; font-style:italic; color:#6495ed;">Optional</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;">Select Conservation Weight Scaling Factor</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;">(Default = 1)</p></body></html>
Signal Propagation
:/icons/transmit.png
220
210
75
24
background-color: #FFFFCC;
border-style: outset;
border-width: 2.1px;
border-radius: 10px;
border-color: white;
font: bold 10px;
color: gray;
min-width: 10em;
padding: 6px;
back
:/icons/control_start_blue.png
310
210
75
24
background-color: #FFFFCC;
border-style: outset;
border-width: 2.1px;
border-radius: 10px;
border-color: white;
font: bold 10px;
color: gray;
min-width: 10em;
padding: 6px;
submit
:/icons/layers.png
110
170
203
31
255
218
7
170
170
255
143
146
147
255
218
7
170
170
255
143
146
147
106
104
100
143
146
147
143
146
147
true
QFrame::Panel
QFrame::Plain
2
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-size:10pt; font-weight:600; color:#f0ffff;"> Please be patient</span></p></body></html>
280
170
31
31
:/icons/hourglass.png
110
140
201
31
83
152
255
170
170
255
226
202
220
83
152
255
170
170
255
226
202
220
106
104
100
226
202
220
226
202
220
Comic Sans MS
14
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Comic Sans MS'; font-size:14pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2'; font-size:8pt;"> <span style=" font-weight:600; color:#6495ed;">Calculation in Progress</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2'; font-size:8pt; font-weight:600; color:#6495ed;"> (This will take 3-10 minutes)</p></body></html>
20
20
365
111
Pathway Start and End
25
20
71
28
Select Initial
Residue
286
20
61
28
Select Final
Residue
110
20
158
31
Max Distance Between Adjacent
Residues (Angstrom)
145
88
91
16
131
135
135
131
135
135
127
127
127
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal; text-decoration:none;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:8pt;"><span style=" font-weight:600; font-style:italic; color:#6495ed;">Default = 3.25 A</span></p></body></html>
27
60
51
22
9999
1
165
60
51
22
5.000000000000000
0.000000000000000
0.050000000000000
3.250000000000000
287
60
51
22
9999
1