-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathtest.html
191 lines (88 loc) · 13 KB
/
test.html
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
<!DOCTYPE html>
<html lang="en">
<head>
<title>1 shared paper | Paperpile</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, minimum-scale=1.0, maximum-scale=1.0, user-scalable=no" />
<meta name="robots" content="noindex, nofollow">
<meta content="Paperpile" property="og:site_name" />
<meta content="Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures" property="og:title" />
<meta content="Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures" name="twitter:title" />
<meta content="Kolodny R, et al. J. Mol. Biol., 2005 ABSTRACT: We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called "Best-of-All" that combines the best results of all methods. Many commonly used methods miss 10-50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution." property="og:description" />
<meta content="Kolodny R, et al. J. Mol. Biol., 2005 ABSTRACT: We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called "Best-of-All" that combines the best results of all methods. Many commonly used methods miss 10-50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution." name="twitter:description" />
<meta name="twitter:image" content="https://paperpile.com/resources/website/images/logo-p.png" />
<link href="https://fonts.googleapis.com/css?family=Open+Sans:400,700" rel="stylesheet" type="text/css">
<link rel="stylesheet" type="text/css" href="https://d36wwddjd21ld7.cloudfront.net/resources/css/website.css?v=227" />
<link rel="shortcut icon" href="/resources/images/favicon.ico" />
</head>
<body>
<!-- Navigation bar -->
<div class="navbar navbar-default navbar-fixed-top pp-navbar">
<div class="container-fluid">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-controls="navbar" role="button">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a href="/welcome"><img class="logo-small" src="https://d36wwddjd21ld7.cloudfront.net/resources/website/images/logo-small-black.png?v=227" alt="Paperpile logo"></a>
</div>
<div id="navbar" class="collapse navbar-collapse ">
<ul class="nav navbar-nav navbar-right" >
<li class="tab nav-sign-up" style="width:140px;">
<a href="/app" class="pp-start-webapp">Open Paperpile</a>
</li>
</ul>
</div>
</div>
</div>
<div class="container-fluid pp-full-width">
<div class="row-fluid">
<div class="span12">
<div class="content-container no-shadow pp-full-width">
<div class="pp-papers-container">
<h1> Andreas Gruber has shared a paper with you</h1>
<div class="container-fluid pricing">
<div class="pricing-table row-fluid">
<div class="pp-pub-item"><div class="pp-pub-title">Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures</div><div class="pp-pub-authors">Kolodny R, Koehl P, Levitt M</div><div class="pp-pub-reference"><span class="pp-pub-journal">J. Mol. Biol.</span>, <span class="pp-pub-year">2005</span><span class="pp-pub-type"> — Journal Article</span></div><div class="pp-pub-links"><a class="pp-pub-view-pdf" target="_blank" href="/shared/Sephwh/download/916c23dd-e1c0-03d0-a3d4-cdea61b235be">View PDF</a> <a class="pp-pub-link" style="margin-right:5px;" target="_blank" href="http://dx.doi.org/10.1016/j.jmb.2004.12.032">Website</a> <span class="pp-pub-abstract-icon pp-pub-abstract-icon-hidden">▶</span><a class="pp-pub-link pp-pub-abstract-toggle">Abstract</a></div><div class="pp-pub-abstract" style="display:none;">We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called "Best-of-All" that combines the best results of all methods. Many commonly used methods miss 10-50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution.</div></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<footer class="container pp-boxed">
<ul>
<li>© 2015 Paperpile LLC</li>
<li><a href="/features">Features</a></li>
<li><a href="/tos">Terms of Service</a></li>
<li><a href="/privacy">Privacy</a></li>
<li><a href="mailto:[email protected]" target="_blank">Support</a></li>
<li><a href="http://twitter.com/paperpile" target="_blank">Follow us</a></li>
</ul>
</footer>
<script type="text/javascript" src="https://d36wwddjd21ld7.cloudfront.net/resources/js/pp-website.js?v=227"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
(function(e,b){if(!b.__SV){var a,f,i,g;window.mixpanel=b;b._i=[];b.init=function(a,e,d){function f(b,h){var a=h.split(".");2==a.length&&(b=b[a[0]],h=a[1]);b[h]=function(){b.push([h].concat(Array.prototype.slice.call(arguments,0)))}}var c=b;"undefined"!==typeof d?c=b[d]=[]:d="mixpanel";c.people=c.people||[];c.toString=function(b){var a="mixpanel";"mixpanel"!==d&&(a+="."+d);b||(a+=" (stub)");return a};c.people.toString=function(){return c.toString(1)+".people (stub)"};i="disable time_event track track_pageview track_links track_forms register register_once alias unregister identify name_tag set_config people.set people.set_once people.increment people.append people.union people.track_charge people.clear_charges people.delete_user".split(" ");
for(g=0;g<i.length;g++)f(c,i[g]);b._i.push([a,e,d])};b.__SV=1.2;a=e.createElement("script");a.type="text/javascript";a.async=!0;a.src="undefined"!==typeof MIXPANEL_CUSTOM_LIB_URL?MIXPANEL_CUSTOM_LIB_URL:"file:"===e.location.protocol&&"//cdn.mxpnl.com/libs/mixpanel-2-latest.min.js".match(/^\/\//)?"https://cdn.mxpnl.com/libs/mixpanel-2-latest.min.js":"//cdn.mxpnl.com/libs/mixpanel-2-latest.min.js";f=e.getElementsByTagName("script")[0];f.parentNode.insertBefore(a,f)}})(document,window.mixpanel||[]);mixpanel.init("ec1c5f1d73427aaeb0d69958a8f79d7f");
mixpanel.identify("[email protected]");
ga('create', 'UA-40084785-1', {
'cookieDomain': 'paperpile.com',
// We do per-request sampling of data within Paperpile, so we want
// to track 100% of users
'siteSpeedSampleRate': 100,
'sampleRate': 100
});
var loginStatus;
loginStatus = 'Signed-up';
ga('set', 'dimension1', loginStatus);
ga('send', 'pageview', { 'hitCallback': function(){if (window.PPW) { PPW.removeUtms(); } } });
</script>
</body>
</html>