-
Notifications
You must be signed in to change notification settings - Fork 2
Expand file tree
/
Copy pathindex.html
More file actions
213 lines (182 loc) · 7.6 KB
/
Copy pathindex.html
File metadata and controls
213 lines (182 loc) · 7.6 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="">
<meta name="author" content="">
<link rel="icon" href="imgs/favicon.ico">
<title>GetContacts</title>
<!-- Highlight.js -->
<link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css">
<script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
<!-- Bootstrap core CSS -->
<!--<link href="vendor/bootstrap/bootstrap.min.css" rel="stylesheet">-->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css">
<!-- Fontawesome icons -->
<script defer src="https://use.fontawesome.com/releases/v5.0.8/js/all.js"></script>
<!-- Custom styles for this template -->
<link href="css/base.css" rel="stylesheet">
<link href="css/recipe-list.css" rel="stylesheet">
<style>
</style>
</head>
<body>
<!-- Jumbotron and menu -->
<header>
<div class="jumbotron">
<div class="container">
<h1 class="display-3"><a href="index.html">GetContacts</a></h1>
<p>Interaction analysis for molecular structures and ensembles</p>
</div>
<nav class="navbar navbar-default">
<div class="container">
<ul class="nav navbar-nav">
<li class="nav-item"><a class="nav-link" href="index.html">Home</a></li>
<li class="nav-item"><a class="nav-link" href="getting_started.html">Installation</a></li>
<li class="nav-item"><a class="nav-link" href="interactions.html">Interaction types</a></li>
<li class="nav-item">
<a class="nav-link" href="https://github.com/getcontacts/getcontacts">
Github <i class="fab fa-github"></i>
</a>
</li>
<li class="nav-item">
<a class="nav-link" href="https://docs.google.com/presentation/d/1HmN9AuU4gL-jMlJdR6cMleueQ-nRWOE_hiWtO8OQEoo/edit?usp=sharing">
Intro slides <img src="imgs/jumbo/GSlides.png" style="height:14px;margin-bottom:2px">
</a>
</li>
</ul>
</div>
</nav>
</div>
</header>
<div class="container">
<p>
Virtually all fundamental biological processes are driven by proteins. The molecular
functions of proteins (e.g. ligand-binding) are governed by networks of molecular interactions such as
hydrogen bonds and van der Waals interactions
</p>
<div class="panel panel-default">
<div class="panel-body">
<ul style="margin-bottom:0px">
<li>Which are the key residues and interactions in your protein?</li>
<!--<li>What are the most prominent commonalities and differences between interactions in different conditions?</li>-->
<li>How do these interactions change under different states and conditions?</li>
<!--<li>How does the interaction network evolve in computational simulations?</li>-->
</ul>
</div>
</div>
<p>
Answer these questions and many other such questions using 'getcontacts' - a package developed
exclusively to dissect and visualize molecular interactions from structures and dynamics of proteins.
GetContacts is equipped to handle structures and dynamics data from a variety of technologies including X-ray
crystallography, NMR, Cryo-EM, and MD simulations.
</p>
</div>
<div class="container">
<!--<div class="panel panel-primary">-->
<!--<div class="panel-heading">Recipes</div>-->
<!--<div class="panel-body">-->
<h3>Recipes</h3>
<div class="row">
<div class="col-md-6 recipe">
<a href="static_to_fingerprints.html">
<div class="recipe-thumb">
<img src="imgs/recipeicons/two-panel_singles-to-freq.png">
</div>
<h4>Compare interactions across static structures</h4>
</a>
<p>Example applications:</p>
<ul class="recipe-bullet">
<li>- Contact networks of proteins from different experimental conditions</li>
</ul>
</div>
<div class="col-md-6 recipe">
<a href="trajectory_to_fingerprints.html">
<div class="recipe-thumb">
<img src="imgs/recipeicons/two-panel_sim-to-freq.gif">
</div>
<h4>Compare interactions across simulations/ensembles</h4>
</a>
<p>Example applications:</p>
<ul class="recipe-bullet">
<li>- Compare interaction network of the same receptor with different ligands</li>
<li>- Compare interaction network of protein in different conditions (solvation, salt-concentration,
phosphorylation etc.)</li>
</ul>
</div>
<div class="col-md-6 recipe">
<a href="trajectory_to_ticc.html">
<div class="recipe-thumb">
<img src="imgs/recipeicons/two-panel_onesim-ticc.gif">
</div>
<h4>Identify and compare simulation substate contacts</h4>
</a>
<p>Example applications:</p>
<ul class="recipe-bullet">
<li>- Identify substates in MCMC simulations</li>
<li>- Characterize ligand binding pocket poses</li>
</ul>
</div>
<div class="col-md-6 recipe">
<a href="family_flare.html">
<div class="recipe-thumb">
<img src="imgs/recipeicons/family-flare.png">
</div>
<h4>Protein family interaction comparison</h4>
</a>
<p>Example applications:</p>
<ul class="recipe-bullet">
<li>- Identify stabilizing interactions within GPCR families</li>
<li>- Make large-scale interaction analysis of any PFAM subfamily</li>
</ul>
</div>
<div class="col-md-6 recipe">
<a href="trajectory_to_flare.html">
<div class="recipe-thumb">
<img src="imgs/recipeicons/md_to_flare.gif">
</div>
<h4>Interactive flareplot from trajectory</h4>
</a>
<p>Example applications:</p>
<ul class="recipe-bullet">
<li>- Explore interactions in trajectory</li>
<li>- Preview and evaluate substates</li>
</ul>
</div>
</div>
</div>
<footer class="container">
<hr>
<div class="row">
<div class="col-md-4" style="text-align: center">
<i class="far fa-copyright"></i> Stanford and authors 2016-2018
</div> <!-- class="col-md-4" -->
<div class="col-md-4" style="text-align: center">
<a href="https://github.com/getcontacts/getcontacts/issues">
<i class="fab fa-github"></i> Submit request and issues
</a>
</div> <!-- class="col-md-4" -->
<div class="col-md-4" style="text-align: center">
<a href="https://gpcrviz.slack.com">
<i class="fab fa-slack"></i> Join us on slack
</a>
</div> <!-- class="col-md-4" -->
</div> <!-- class="row" -->
</footer>
<script>hljs.initHighlightingOnLoad();</script>
<!-- Bootstrap core JavaScript
================================================== -->
<!-- Placed at the end of the document so the pages load faster -->
<script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
<script>window.jQuery || document.write('<script src="../../../../assets/js/vendor/jquery-slim.min.js"><\/script>')</script>
<!--<script src="../../../../assets/js/vendor/popper.min.js"></script>-->
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js"></script>
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<script>
$(function () {
$('[data-toggle="tooltip"]').tooltip()
})
</script>
</body>
</html>