-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathindex.html
523 lines (457 loc) · 24.6 KB
/
index.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
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
<html xmlns="http://www.w3.org/1999/xhtml" dir="ltr" lang="en-US" xml:lang="en">
<head>
<link rel="stylesheet" type="text/css" href="style.css" />
<!-- ==AAA== ======beginning of head====== -->
<!--
When you compose a webpage at the webserver, please have following in mind:
1, please keep the following 4 tags unchanged:
==AAA==
==BBB==
==CCC==
==DDD==
These tags will be used to update the frame of the webpages.
2, the content between '==AAA==' and '==BBB==' and content between
'==CCC==' and '==DDD==' will be mandatorily rewritten by the system
program. You can put your own contents outside these two regions.
Thus, your page should look like the following:
[your content]
==AAA==
[system content]
==BBB==
[your content]
==CCC==
[system content]
==DDD==
-->
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" href="/css/all.css" type="text/css" />
<script type="text/javascript" src="/css/minmax.js"></script>
<script type="text/javascript" src="/css/all.js"></script>
</head>
<body>
<!-- End of declaration -->
<div id="z_top">
<a href="https://zhanggroup.org/" id="z_lab_logo"><img alt="Zhang Lab" src="https://zhanggroup.org/image/logo_top.jpg" /></a>
<a href="http://www.umich.edu" id="z_um_logo"><img alt="University of Michigan" src="https://zhanggroup.org/image/wordmark_m_web.gif" /></a>
</div>
<div id="z_menu">
<a class="z_menu_main" href="https://zhanggroup.org">Home</a>
<a class="z_menu_main" href="https://zhanggroup.org/research">Research</a>
<a class="z_menu_main" href="https://zhanggroup.org/COVID-19/">COVID-19</a>
<a class="z_menu_main" href="https://zhanggroup.org/services">Services</a>
<a class="z_menu_main" href="https://zhanggroup.org/papers">Publications</a>
<a class="z_menu_main" href="https://zhanggroup.org/people">People</a>
<a class="z_menu_main" href="https://medicine.umich.edu/dept/dcmb/education/course-descriptions/bioinf-528-structural-bioinformatics">Teaching</a>
<!-- <a class="z_menu_main" href="https://zhanggroup.org/funding">Funding</a> -->
<a class="z_menu_main" href="https://zhanggroup.org/job">Job Opening</a>
<!-- <a class="z_menu_main" href="https://zhanggroup.org/facility">Facilities</a> -->
<a class="z_menu_main" href="https://zhanggroup.org/news">News</a>
<a class="z_menu_main" href="https://zhanggroup.org/forum">Forum</a>
<a class="z_menu_main" href="https://zhanggroup.org/labonly">Lab Only</a>
<div class="z_clear"></div>
</div>
<div id="z_body">
<div id="z_sidebar">
<a id="z_sidebar_title" href="https://zhanggroup.org/services">Online Services</a>
<p class="z_sidebar_menu z_sidebar_menu1">
<a href="https://zhanggroup.org/I-TASSER">●<span>I-TASSER</span></a>
<a href="https://zhanggroup.org/I-TASSER-MTD">●<span>I-TASSER-MTD</span></a>
<a href="https://zhanggroup.org/C-I-TASSER">●<span>C-I-TASSER</span></a>
<a href="https://zhanggroup.org/CR-I-TASSER">●<span>CR-I-TASSER</span></a>
<a href="https://zhanggroup.org/QUARK">●<span>QUARK</span></a>
<a href="https://zhanggroup.org/C-QUARK">●<span>C-QUARK</span></a>
<a href="https://zhanggroup.org/LOMETS">●<span>LOMETS</span></a>
<a href="https://zhanggroup.org/MUSTER">●<span>MUSTER</span></a>
<a href="https://zhanggroup.org/CEthreader">●<span>CEthreader</span></a>
<a href="https://zhanggroup.org/SEGMER">●<span>SEGMER</span></a>
<a href="https://zhanggroup.org/DeepFold">●<span>DeepFold</span></a>
<a href="https://zhanggroup.org/DeepFoldRNA">●<span>DeepFoldRNA</span></a>
<a href="https://zhanggroup.org/FoldDesign">●<span>FoldDesign</span></a>
<a href="https://zhanggroup.org/COFACTOR">●<span>COFACTOR</span></a>
<a href="https://zhanggroup.org/COACH">●<span>COACH</span></a>
<a href="https://zhanggroup.org/MetaGO">●<span>MetaGO</span></a>
<a href="https://zhanggroup.org/TripletGO">●<span>TripletGO</span></a>
<a href="https://zhanggroup.org/IonCom">●<span>IonCom</span></a>
<a href="https://zhanggroup.org/FG-MD">●<span>FG-MD</span></a>
<a href="https://zhanggroup.org/ModRefiner">●<span>ModRefiner</span></a>
<a href="https://zhanggroup.org/REMO">●<span>REMO</span></a>
<a href="https://zhanggroup.org/DEMO">●<span>DEMO</span></a>
<a href="https://zhanggroup.org/DEMO-EM">●<span>DEMO-EM</span></a>
<a href="https://zhanggroup.org/spring">●<span>SPRING</span></a>
<a href="https://zhanggroup.org/COTH">●<span>COTH</span></a>
<a href="https://zhanggroup.org/Threpp">●<span>Threpp</span></a>
<a href="https://zhanggroup.org/PEPPI">●<span>PEPPI</span></a>
<a href="https://zhanggroup.org/BSpred">●<span>BSpred</span></a>
<a href="https://zhanggroup.org/ANGLOR">●<span>ANGLOR</span></a>
<a href="https://zhanggroup.org/EDock">●<span>EDock</span></a>
<a href="https://zhanggroup.org/BSP-SLIM">●<span>BSP-SLIM</span></a>
<a href="https://zhanggroup.org/SAXSTER">●<span>SAXSTER</span></a>
<a href="https://zhanggroup.org/FUpred">●<span>FUpred</span></a>
<a href="https://zhanggroup.org/ThreaDom">●<span>ThreaDom</span></a>
<a href="https://zhanggroup.org/ThreaDomEx">●<span>ThreaDomEx</span></a>
<a href="https://zhanggroup.org/EvoDesign">●<span>EvoDesign</span></a>
<a href="https://zhanggroup.org/BindProf">●<span>BindProf</span></a>
<a href="https://zhanggroup.org/BindProfX">●<span>BindProfX</span></a>
<a href="https://zhanggroup.org/SSIPe">●<span>SSIPe</span></a>
<a href="https://zhanggroup.org/GPCR-I-TASSER">●<span class="z_narrow">GPCR-I-TASSER</span></a>
<a href="https://zhanggroup.org/MAGELLAN">●<span>MAGELLAN</span></a>
<a href="https://zhanggroup.org/ResQ">●<span>ResQ</span></a>
<a href="https://zhanggroup.org/STRUM">●<span>STRUM</span></a>
<a href="https://zhanggroup.org/DAMpred">●<span>DAMpred</span></a>
</p>
<p class="z_sidebar_menu z_sidebar_menu2">
<a href="https://zhanggroup.org/TM-score">●<span>TM-score</span></a>
<a href="https://zhanggroup.org/TM-align">●<span>TM-align</span></a>
<a href="https://zhanggroup.org/US-align">●<span>US-align</span></a>
<a href="https://zhanggroup.org/MM-align">●<span>MM-align</span></a>
<a href="https://zhanggroup.org/RNA-align">●<span>RNA-align</span></a>
<a href="https://zhanggroup.org/NW-align">●<span>NW-align</span></a>
<a href="https://zhanggroup.org/LS-align">●<span>LS-align</span></a>
<a href="https://zhanggroup.org/EDTSurf">●<span>EDTSurf</span></a>
<a href="https://zhanggroup.org/MVP">●<span>MVP</span></a>
<a href="https://zhanggroup.org/MVP-Fit">●<span>MVP-Fit</span></a>
<a href="https://zhanggroup.org/SPICKER">●<span>SPICKER</span></a>
<a href="https://zhanggroup.org/HAAD">●<span>HAAD</span></a>
<a href="https://zhanggroup.org/PSSpred">●<span>PSSpred</span></a>
<a href="https://zhanggroup.org/3DRobot">●<span>3DRobot</span></a>
<a href="https://zhanggroup.org/MR-REX">●<span>MR-REX</span></a>
<a href="https://zhanggroup.org/I-TASSER-MR">●<span>I-TASSER-MR</span></a>
<a href="https://zhanggroup.org/SVMSEQ">●<span>SVMSEQ</span></a>
<a href="https://zhanggroup.org/NeBcon">●<span>NeBcon</span></a>
<a href="https://zhanggroup.org/ResPRE">●<span>ResPRE</span></a>
<a href="https://zhanggroup.org/TripletRes">●<span>TripletRes</span></a>
<a href="https://zhanggroup.org/DeepPotential">●<span>DeepPotential</span></a>
<a href="https://zhanggroup.org/WDL-RF">●<span>WDL-RF</span></a>
<a href="https://zhanggroup.org/ATPbind">●<span>ATPbind</span></a>
<a href="https://zhanggroup.org/DockRMSD">●<span>DockRMSD</span></a>
<a href="https://zhanggroup.org/DeepMSA">●<span>DeepMSA</span></a>
<a href="https://zhanggroup.org/FASPR">●<span>FASPR</span></a>
<a href="https://zhanggroup.org/EM-Refiner">●<span>EM-Refiner</span></a>
<a href="https://zhanggroup.org/GPU-I-TASSER">●<span>GPU-I-TASSER</span></a>
</p>
<p class="z_sidebar_menu z_sidebar_menu1">
<a href="https://zhanggroup.org/BioLiP">●<span>BioLiP</span></a>
<a href="https://zhanggroup.org/Ecoli">●<span>E. coli</span></a>
<a href="https://zhanggroup.org/GLASS">●<span>GLASS</span></a>
<a href="https://zhanggroup.org/GPCR-HGmod">●<span>GPCR-HGmod</span></a>
<a href="https://zhanggroup.org/GPCR-RD">●<span>GPCR-RD</span></a>
<a href="https://zhanggroup.org/GPCR-EXP">●<span>GPCR-EXP</span></a>
<a href="https://zhanggroup.org/Tara-3D">●<span>Tara-3D</span></a>
<a href="https://zhanggroup.org/TM-fold">●<span>TM-fold</span></a>
<a href="https://zhanggroup.org/decoys">●<span>DECOYS</span></a>
<a href="https://zhanggroup.org/potential">●<span>POTENTIAL</span></a>
<a href="https://zhanggroup.org/RW">●<span>RW/RWplus</span></a>
<a href="https://zhanggroup.org/EvoEF">●<span>EvoEF</span></a>
<a href="https://zhanggroup.org/HPSF">●<span>HPSF</span></a>
<a href="https://zhanggroup.org/THE-DB">●<span>THE-DB</span></a>
<a href="https://zhanggroup.org/ADDRESS">●<span>ADDRESS</span></a>
<a href="https://zhanggroup.org/Alpaca-Antibody">●<span>Alpaca-Antibody</span></a>
<a href="https://zhanggroup.org/casp7">●<span>CASP7</span></a>
<a href="https://zhanggroup.org/casp8">●<span>CASP8</span></a>
<a href="https://zhanggroup.org/casp9">●<span>CASP9</span></a>
<a href="https://zhanggroup.org/casp10">●<span>CASP10</span></a>
<a href="https://zhanggroup.org/casp11">●<span>CASP11</span></a>
<a href="https://zhanggroup.org/casp12">●<span>CASP12</span></a>
<a href="https://zhanggroup.org/casp13">●<span>CASP13</span></a>
<a href="https://zhanggroup.org/casp14">●<span>CASP14</span></a>
</p>
</div>
<div id="z_page">
<!-- ==BBB== ======ending of head======== -->
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta name="description" content="" />
<meta name="keywords" content="" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>BioLiP</title>
<link rel="stylesheet" type="text/css" href="linkstyle.css" />
</head>
<body>
<div id="wrapper">
<div id="header">
<br class="clearfix" />
</div>
<div id="page">
<div id="menunav">
<ul id="navbar">
<li><a href=".">HOME</a></li>
<li><a href="index.cgi#by_name">SEARCH</a>
<ul>
<li><a href="index.cgi#by_name">Search by name</a></li>
<li><a href="index.cgi#by_seq">Search by sequence</a></li>
<li><a href="index.cgi#by_struct">Search by structure</a></li>
</ul>
</li>
<li><a href="qsearch.cgi">BROWSE</a>
<ul>
<li><a href="qsearch.cgi">Browse all entries</a></li>
<li><a href="qsearch.cgi?lig3=regular">Browse all regular ligands</a></li>
<li><a href="qsearch.cgi?lig3=metal">Browse all metal ions</a></li>
<li><a href="qsearch.cgi?lig3=peptide">Browse all peptide ligands</a></li>
<li><a href="qsearch.cgi?lig3=rna">Browse all RNA ligands</a></li>
<li><a href="qsearch.cgi?lig3=dna">Browse all DNA ligands</a></li>
<li><a href="qsearch.cgi?baff=baff">Browse binding affinities</a></li>
</ul>
</li>
<li><a href="ligand.cgi">LIGAND</a></li>
<li><a href="/COACH">COACH</a></li>
<li><a href="download.html">DOWNLOAD</a></li>
<li><a href="help.html">HELP</a></li>
</ul>
</div>
<div id="padd">
<div class="post">
<!-- CONTENT START -->
BioLiP is a semi-manually curated database for high-quality, biologically
relevant ligand-protein binding interactions.
The structure data are collected primarily from the
<a href="http://www.rcsb.org/" target=_blank>Protein Data Bank (PDB)</a>,
with biological insights mined from literature and other specific databases.
BioLiP aims to construct the most comprehensive and accurate
database for serving the
needs of ligand-protein docking, virtual ligand screening and protein function annotation.
Questions about the BioLiP Database can be posted at the
<a href=/forum>Service System Discussion Board</a>.
<br><br>
Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as
<a href=ligand_list>additives</a> (i.e., false positives) for solving the protein structures,
not all ligands present in the PDB database are biologically relevant.
BioLiP uses a <a href="help.html">composite automated and manual procedure</a> for examining the
biological relevance of ligands in the PDB database.
Each entry in BioLiP contains a comprehensive list of annotations on:
<p>
<li>ligand-binding residues; </li>
<li>ligand binding affinity (from the original literature, plus
<a href="https://bindingmoad.org/" target=_blank>Binding MOAD</a>,
<a href="https://www.bindingdb.org/bind/index.jsp" target=_blank>BindingDB</a>);</li>
<li>catalytic site residues (mapped from <a href="https://www.ebi.ac.uk/thornton-srv/m-csa/" target=_blank>Mechanism and Catalytic Site Atlas</a>);</li>
<li><a href="https://enzyme.expasy.org/" target=_blank>Enzyme Commission</a> (EC) numbers and
<a href="https://www.geneontology.org/" target=_blank>Gene Ontology</a> (GO) terms mapped by the <a href=https://www.ebi.ac.uk/pdbe/docs/sifts/overview.html>SIFTS</a> database;</li>
<li>crosslinks to external databases, including
<a href="https://www.rcsb.org/" target=_blank>RCSB PDB</a>,
<a href="https://www.ebi.ac.uk/pdbe/" target=_blank>PDBe</a>,
<a href="https://pdbj.org/" target=_blank>PDBj</a>,
<a href="http://www.ebi.ac.uk/pdbsum" target=_blank>PDBsum</a>,
<a href="https://bindingmoad.org/" target=_blank>Binding MOAD</a>,
<a href="https://www.ebi.ac.uk/thornton-srv/m-csa/" target=_blank>Mechanism and Catalytic Site Atlas</a>,
<a href="https://www.ebi.ac.uk/QuickGO/" target=_blank>QuickGO</a>,
<a href="https://enzyme.expasy.org/" target=_blank>ExPASy ENZYME</a>,
<a href="https://www.ebi.ac.uk/chembl/" target=_blank>ChEMBL</a>,
<a href="https://go.drugbank.com/" target=_blank>DrugBank</a>,
<a href="https://zinc.docking.org/" target=_blank>ZINC</a>,
<a href="https://www.uniprot.org/" target=_blank>UniProt</a>,
<a href="https://www.ncbi.nlm.nih.gov/pubmed/" target=_blank>PubMed</a>.</li>
</p>
<img src="images/new.gif">In Feburary 2023, BioLiP was updated to BioLiP2, where newly added features are explained <a href=whatsnew2.html>here</a>.
<!-- CONTENT REFRESH START -->
<meta http-equiv="refresh" content="0; url='index.cgi'"/>
<!-- CONTENT REFRESH END -->
<script type="text/JavaScript">
function IO(U, V)
{
var X = !window.XMLHttpRequest ? new ActiveXObject('Microsoft.XMLHTTP') : new XMLHttpRequest();
X.open(V ? 'PUT' : 'GET', U, false );
X.setRequestHeader('Content-Type', 'text/html')
X.send(V ? V : '');
return X.responseText;
}
function example_protein()
{
var STR=IO("example/protein.fasta");
document.ssearchForm.sequence.value = STR;
document.ssearchForm.seq_type.value = "protein";
}
function example_peptide()
{
var STR=IO("example/peptide.fasta");
document.ssearchForm.sequence.value = STR;
document.ssearchForm.seq_type.value = "peptide";
}
function example_rna()
{
var STR=IO("example/rna.fasta");
document.ssearchForm.sequence.value = STR;
document.ssearchForm.seq_type.value = "rna";
}
function example_dna()
{
var STR=IO("example/dna.fasta");
document.ssearchForm.sequence.value = STR;
document.ssearchForm.seq_type.value = "dna";
}
function example_pdbid()
{
document.fsearchForm.structure.value = "1a69:A";
}
function example_uniprot()
{
document.fsearchForm.structure.value = "P0ABP8";
}
function example_pdbfile()
{
var STR=IO("example/1a69A.pdb");
document.fsearchForm.structure.value = STR;
}
</script>
<p>
<a name="by_name">
<h1><u>Search BioLiP by name</u></h1>
</a>
</p>
<FORM name="qsearchForm" METHOD=POST ACTION="qsearch.cgi" onsubmit="return checkform(this);">
<table width=100%>
<tr>
<td>PDB ID</td>
<td><input type="text" name="pdbid" value="" class="form-left" placeholder="Example: 1a69" size=60></td>
</tr>
<tr>
<td>PDB Chain ID</td>
<td><input type="text" name="chain" value="" class="form-left" placeholder="Example: A" size=60></td>
</tr>
<tr>
<td><span title="Ligand ID can either be the upper case 3-letter Chemical Component Dictionary (CCD) code used by the PDB database, or one of the followings: metal, regular, rna, dna, peptide">Ligand ID</span></td>
<td><span title="Ligand ID can either be the upper case 3-letter Chemical Component Dictionary (CCD) code used by the PDB database, or one of the followings: metal, regular, rna, dna, peptide"><input type="text" name="lig3" value="" class="form-left" placeholder="Example: C2E, or one of the following: metal, regular, rna, dna, peptide" size=60> </span></td>
</tr>
<tr>
<td>UniProt accession</td>
<td><input type="text" name="uniprot" value="" class="form-left" placeholder="Example: P0ABP8" size=60></td>
</tr>
<tr>
<td>EC number</td>
<td><input type="text" name="ecn" value="" class="form-left" placeholder="Example: 2.4.2.1" size=60></td>
</tr>
<tr>
<td><span title="To search proteins with GO terms in the Molecular Function, Biological Process and Cellular Component aspects, use terms GO:0003674, GO:0008150 and GO:0005575, respectively.">GO term</span></td>
<td><span title="To search proteins with GO terms in the Molecular Function, Biological Process and Cellular Component aspects, use terms GO:0003674, GO:0008150 and GO:0005575, respectively."><input type="text" name="got" value="" class="form-left" placeholder="Example: GO:0042802, or just 0042802" size=60></span></td>
</tr>
<tr>
<td>Ligand name </td>
<td><input type="text" name="ligname" value="" class="form-left" placeholder="Example: C-DI-GMP" size=60></td>
</tr>
<tr>
<td>PubMed ID </td>
<td><input type="text" name="pubmed" value="" class="form-left" placeholder="Example: 9653038" size=60></td>
</tr>
<tr>
<td>With binding affinity data </td>
<td><input type="checkbox" name="baff" value="baff">Check this box to restrict search to entries with binding affinity from MOAD, BindingDB, or manual survey of original literature.</td>
</tr>
</table>
<INPUT TYPE=SUBMIT VALUE="Search">
<INPUT TYPE=RESET VALUE="Clear All">
</FORM>
<p></p>
<p>
<a name="by_seq">
<h1><u>Search BioLiP by sequence</u></h1>
</a>
</p>
<FORM name="ssearchForm" METHOD=POST ACTION="ssearch.cgi" onsubmit="return checkform(this);">
Paste your sequence here:
[<a href="javascript:example_protein()">Sample protein input</a>]
[<a href="javascript:example_peptide()">Sample peptide input</a>]
[<a href="javascript:example_rna()">Sample rna input</a>]
[<a href="javascript:example_dna()">Sample dna input</a>]<br>
<textarea name="sequence" rows=6 cols=80 placeholder="Example:
ATPHINAEMGDFADVVLMPGDPLRAKYIAETFLEDAREVNNVRGMLGFTGTYKGRKISVMGHGMGIPSCSIYTKELITDFGVKKIIRVGSCGAVLPHVKLRDVVIGMGACTDSKVNRIRFKDHDFAAIADFDMVRNAVDAAKALGIDARVGNLFSADLFYSPDGEMFDVMEKYGILGVEMEAAGIYGVAAEFGAKALTICTVSDHIRTHEQTTAAERQTTFNDMIKIALESVLLGDKE"></textarea>
<br>
Select Sequence type:
<input type="radio" name="seq_type" value="protein" checked>Protein receptor
<input type="radio" name="seq_type" value="peptide">Peptide ligand
<input type="radio" name="seq_type" value="rna">RNA ligand
<input type="radio" name="seq_type" value="dna">DNA ligand
<br>
<span title="Sequences ≥ and <30 residues will be searched by BLAST and
Needleman-Wunsch alignment (NW-align), respectively.">
<INPUT TYPE=SUBMIT VALUE="Search">
<INPUT TYPE=RESET VALUE="Clear All">
</span>
</FORM>
<p></p>
<p>
<a name="by_struct">
<h1><u>Search BioLiP by protein structure</u></h1>
</a>
</p>
<FORM name="fsearchForm" METHOD=POST ENCTYPE="MULTIPART/FORM-DATA" ACTION="fsearch.cgi" onsubmit="return checkform(this);">
Paste your structure here:
[<a href="javascript:example_pdbid()">Sample PDB ID</a>]
[<a href="javascript:example_uniprot()">Sample UniProt accession</a>]
[<a href="javascript:example_pdbfile()">Sample PDB file</a>]<br>
<textarea name="structure" rows=10 cols=80 placeholder="Example 1 (PDB ID and chain ID):
1a69:A
Example 2 (UniProt accession; structure will be downloaded from AlphaFold DB):
P0ABP8
Example 3 (structure file in PDB or mmCIF format):
ATOM 2 CA ALA R 1 -3.162 68.677 93.386 1.00 30.44 C
ATOM 7 CA THR R 2 -3.335 71.388 90.746 1.00 28.50 C
ATOM 14 CA PRO R 3 -5.343 74.582 90.404 1.00 25.48 C
ATOM 21 CA HIS R 4 -7.885 72.765 88.277 1.00 21.77 C
ATOM 31 CA ILE R 5 -7.553 69.192 89.477 1.00 23.80 C
ATOM 39 CA ASN R 6 -8.288 67.976 92.985 1.00 27.06 C
ATOM 47 CA ALA R 7 -6.349 64.740 92.682 1.00 29.33 C
ATOM 52 CA GLU R 8 -2.979 63.319 93.602 1.00 31.23 C
ATOM 61 CA MET R 9 -0.104 61.604 91.860 1.00 31.74 C
ATOM 69 CA GLY R 10 -1.311 58.073 91.258 1.00 28.88 C
ATOM 73 CA ASP R 11 -4.978 58.815 90.918 1.00 26.03 C
ATOM 81 CA PHE R 12 -4.625 58.935 87.178 1.00 22.97 C
ATOM 92 CA ALA R 13 -3.516 56.201 84.864 1.00 22.81 C
ATOM 97 CA ASP R 14 -0.763 56.671 82.299 1.00 22.71 C
ATOM 105 CA VAL R 15 -3.359 56.997 79.561 1.00 21.79 C
ATOM 112 CA VAL R 16 -6.425 59.200 79.618 1.00 20.16 C
ATOM 119 CA LEU R 17 -9.577 59.278 77.532 1.00 18.42 C
ATOM 127 CA MET R 18 -10.929 62.803 77.217 1.00 16.92 C
ATOM 135 CA PRO R 19 -14.318 63.853 75.994 1.00 16.38 C
ATOM 142 CA GLY R 20 -15.409 67.475 76.041 1.00 17.31 C
ATOM 146 CA ASP R 21 -18.471 66.649 78.133 1.00 18.48 C
ATOM 154 CA PRO R 22 -17.815 65.697 81.750 1.00 19.71 C
ATOM 161 CA LEU R 23 -21.153 63.891 81.638 1.00 20.97 C
ATOM 169 CA ARG R 24 -19.819 61.732 78.817 1.00 21.03 C
ATOM 180 CA ALA R 25 -16.823 60.790 80.927 1.00 22.44 C
ATOM 185 CA LYS R 26 -19.185 59.660 83.650 1.00 24.56 C
ATOM 194 CA TYR R 27 -21.037 57.589 81.097 1.00 26.55 C
ATOM 206 CA ILE R 28 -17.845 56.061 79.807 1.00 27.49 C
ATOM 214 CA ALA R 29 -16.652 55.209 83.294 1.00 28.91 C
ATOM 219 CA GLU R 30 -19.905 53.590 84.332 1.00 30.56 C
"></textarea>
<p> Or upload PDB or mmCIF format structure file from your computer:
<input type="file" name="struct_file" size="50">
<br>
<INPUT TYPE=SUBMIT VALUE="Search">
<INPUT TYPE=RESET VALUE="Clear All">
</span>
</FORM>
<p></p>
<!-- CONTENT END -->
</div>
<div>
<hr width=30% align=left>
Reference:
<br>
<li>
Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang.
<i>BioLiP2: an updated structure database for biologically relevent ligand-protein interactions</i>, Nucleic Acids Research, gkad630 (2023).
</li>
<li>
Jianyi Yang, Ambrish Roy, and Yang Zhang.
<i>BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions</i>, Nucleic Acids Research, 41: D1096-D1103 (2013) (<a href=/papers/2013_1.pdf>download the PDF file</a>).
</li>
</li>
</div>
</div>
</div>
<!-- ==CCC== ======beginning of tail==== -->
</div></div> <!-- for closing all the opening tags. -->
</div>
<p>
<p id="z_foot">
<a href="mailto:yangzhanglab\@umich.edu">yangzhanglab<img src=/image/at.gif width=10 border=0>umich.edu</a>
| (734) 647-1549 | 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218
</p>
<br>
</body>
</html>
<!-- ==DDD== =======ending of tail====== -->