Appendix

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Appendix

Displayed Antibodies

  • The cDNA of an antibody is cloned and expressed on the surface of macromolecular complexes and individual binders are subsequently selected. The cDNA is generally attached to the macromolecular complex to allow for rapid determination of the sequence of the positive clones. This technology is an alternative to the classical monoclonal antibody method using hybridoma generation from secreting clones.
  • The most common library type is phage display, but other constructs, such as ribosome or yeast display, may be used.
  • The antibody cDNA which is displayed may originate from either naïve or immunized individuals. Non-human libraries are usually immune and human libraries are usually from naïve or naturally exposed individuals, but there are exceptions. The Immunization field should reflect this status when provided by the reference. If the library is derived from a naive subject(s), the Immunization Category should be <Phage Display (No immunization)>. Immune libraries have increased frequency of binders and higher affinity of binding, but naïve libraries are often a source of binders of varied specificities and may be commercially available. Synthetic libraries consist of artificially generated antibody sequences and require a comment in the Comments on Immunization field to clarify what antibodies were used.
  • The type of assays to be entered as contexts are those typically included in other antibody contexts, such as epitope characterization by binding of particular clones. Selection assays (immuno-panning) is not included in the database, unless that data is highly relevant to the subsequent analysis. If needed, this assay type is present under B cell response.
  • The antibody displayed is typically not the entire molecule but the binding fragment. Depending on the cloning procedure, Fab, Fv, scFv or Fab’ fragments may be displayed. This information is to be entered in the Immunoglobulin Domain field. Camelids (camel, dromedary, llama, etc) have a particular IgG isotype devoid of light chains. The binding fragment (variable region of this IgG) is a unique polypeptidic chain named VHH.
  • When the displayed antibody is the material assayed, the Materials Assayed field should be <Displayed Ab(s)> and Antibody Type should be <Display library>. The monoclonoal or polyclonal nature of the antibody will be entered in the Assay Comments field, while the Immunization Comments (if any) should include that the immunization was followed by display library construction.
  • When a recombinant antibody is subsequently expressed in the absence of the displaying particle, the Materials Assayed field should be <Purified immunoglobulin>, the Immunoglobulin Domain field should reflect the fragment used and the Antibody Type field should be <Display library>. As before, the polyclonal or monoclonal nature will be entered in the Assay Comments field with any immunization comments including that the immunization was followed by display library construction.



3D Structural Data

The IEDB includes 3D-structural data describing complexes of epitopes with immune receptor(s): antibodies (or antibody fragments including the variable region), MHC molecules and/or the T cell receptor (or fragments including the antigen recognizing domains).

Exclusions

  • Structures in which the antibody or TCR binds to the epitope outside of the variable antigen-binding region are not curated.
  • Structures in which the MHC molecule binds the epitope outside of the recognition groove are not curated


3D data is captured in the IEDB by structural experts at SDSC when:

  • The structure is obtained by an experimental method.
  • 3D-structure is available in the Protein Data Bank (http://www.rcsb.org)

Each novel structure is captured only once as a context of the epitope which is bound by the immune receptor. That is if an epitope is bound by an antibody and an MHC molecule, two assays will be captured, one for each structure.

If there are different structures describing different contact residues between the epitope and a receptor, each set of differing contact residues is captured as a separate assay.

Standard Abbreviations

The table below (Table 7 ) shows the list of standard abbreviations consolidated from different immunological journals.

Table 7. Consolidated list of standard abbreviations.
# Abbreviation Expansion
1 14C, 3H, 32P, etc. isotopes
2 2D/3D two dimensional/three dimensional
3 2-ME 2-mercaptoethanol
4 Å angstrom
5 A, Ado adenosine*
6 aa amino acid (only with numbers)
7 Ab antibody
8 ABTS 2,2’-azinobis(3-ethylbenzthiazoline-6-sulfonic acid)
9 Ac acetyl
10 ac alternating current
11 ADCC antibody-dependent cell-mediated cytotoxicity
12 Ade adenine
13 af audio frequency
14 Ag antigen
15 AIDS acquired immunodeficiency syndrome
16 Ala alanine
17 AML acute myeloid leukemia
18 AMP, ADP, ATP, dAMP, ddATP, GTP, etc. For the respective 5’ phosphates of adenosine and other nucleosides, add 2’-, 3’-, or 5’- when needed for contrast
19 Amt Amount
20 ANOVA analysis of variance
21 AP-1 activator protein 1
22 APC antigen-presenting cell
23 Approx Approximately
24 Arg arginine
25 Asn asparagine
26 Asp aspartic acid
27 Asx asparagine or aspartic acid
28 at. wt. atomic weight
29 ATP adenosine triphosphate (also ADP, AMP, CMP, CTP, GDP, GMP, GTP, ITP, NTP, TMP, UDP and UTP)
30 ATPase, dGTPase, etc. Adenosine triphosphatase, deoxyguanosine triophosphatase, etc
31 Avg Average
32 AZT 3’-azido-3-deoxythymidine
33 B.P. before present
34 b.p. boiling point
35 BAL Bronchoalveolar lavage
36 BALT bronchus-associated lymphoid tissue
37 BAPTA-AM 1,2-bis(2-aminophenoxy)ethane-N,N,N’,N’-tetraacetic acid acetoxymethyl ester
38 bcc body-centered-cubic
39 BCG Bacillus Calmette Guerin
40 BCR B cell receptor
41 BM Bone marrow
42 bp base pair (only with numbers)
43 BrdU 5-bromo-2’-deoxyuridine
44 BrUra bromouracil
45 BSA bovine serum albumin
46 Bu butyl
47 Bz benzoyl
48 C complement
49 C’ activated complement
50 C region constant region of Ig
51 C, Cyd cytidine*
52 C/EBP CCAAT/enhancer-binding protein
53 Calc., calc calculated
54 cAMP cyclic AMP
55 CCL CC chemokine ligand
56 CCR CC chemokine receptor
57 CD circular dichroism
58 CD cluster of differentiation
59 CD40L CD40 ligand
60 CDC complement-dependent cytotoxicity
61 cDNA complementary DNA
62 CDR complementarity determining region
63 CFA complete Freund’s adjuvant
64 CFSE 5- (and 6-)carboxyfluorescein diacetate succinimidyl ester
65 CFU colony-forming unit
66 cGMP guanosine 3’ 5’-cyclic monophosphate
67 cGy centiGray (only with numbers)
68 CHAPS 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate
69 CHO Chinese hamster ovary
70 Ci Curie (only with numbers)
71 CIITA class II transactivator
72 CLIP class II-associated invariant-chain peptide
73 cm centimeter (only with numbers)
74 CM-cellulose O-carboxymethylcellulose
75 CML chronic myelogenous leukemia
76 CMV cytomegalovirus
77 CNS central nervous system
78 CoA coenzyme A
79 Con A concanavalin A
80 conc. concentration
81 Concn Concentration
82 const constant
83 COSY correlated spectroscopy
84 CP chemically pure
85 CpG cytosine guanine dinucleotide
86 cpm counts per minute (only with numbers)
87 CR Complement receptor
88 CREB cAMP response element binding protein
89 cRNA complementary RNA
90 CSF colony-stimulating factor
91 CTL cytotoxic T lymphocyte
92 CTLA cytolytic T lymphocyte-associated Ag
93 CXCL CXC chemokine ligand
94 CXCR CXC chemokine receptor
95 Cys cysteine or half-cystine
96 Cyt cytosine
97 d deoxy; distilled (as in dH2O)
98 d deoxy (carbohydrates and nucleotides)
99 d day (only with numbers)
100 D region diversity region of Ig or T cell receptor for Ag
101 Da dalton (only with numbers)
102 DAPI 4’ 6-diamidino-2-phenylindole
103 dATP 2’-deoxyadenosine triphosphate
104 dc direct current
105 DC dendritic cell
106 DEAE diethylaminoethyl
107 DEAE-cellulose diethylaminoethylcellulose
108 df degrees of freedom
109 DHFR dihydrofolate reductase
110 Diam Diameter
111 DMEM Dulbecco’s modified Eagle’s medium
112 DMSO dimethylsulfoxide
113 DNA deoxyribonucleic acid
114 DNase deoxyribonuclease
115 DNP dinitrophenyl
116 dNTP 2’-deoxynucleoside 5’-triphosphate
117 dpm disintegrations per minute
118 ds double-stranded (as dsDNA)
119 dT or dThd thymidine (2'-deoxyribosylthymine)*
120 DTH delayed-type hypersensitivity
121 dThd Thymidine
122 DTT dithiothreitol
123 dUrd Deoxyuridine
124 E erythrocyte
125 E. coli Escherichia coli
126 E/T Effector-to-target cell (ratio)
127 E/T ratio effector to target cell ratio
128 E:T ratio effector to target ratio
129 EAE Experimental autoimmune encephalomyelitis
130 EBV Epstein-Barr virus
131 EC50 50% effective concentration
132 ECG electrocardiogram
133 ECL enhanced chemiluminescence
134 ED50 50% effective dose
135 EDTA ethylenediaminetetraacetic acid
136 EGFP enhanced green fluorescent protein
137 EGTA ethylene glycol-bis(b-aminoethyl ester)-N,N,N’,N’-tetraacetic acid
138 ELISA enzyme-linked immunosorbent assay
139 ELISPOT enzyme-linked immunospot
140 EM electron microscopy
141 EMBL European Molecular Biology Laboratory
142 emf electromotive force
143 EMSA electrophoretic mobility shift assay
144 EPR electron paramagnetic resonance
145 equiv. wt. equivalent weight
146 ER endoplasmic reticulum
147 ERK extracellular signal-regulated kinase
148 ESR electron spin resonance
149 EST expressed sequence tag
150 Et ethyl
151 Etd ethidium
152 Exp., exp experiment(al)
153 Expt Experiment
154 Exptl Experimental
155 f.p. freezing point
156 Fab Ag-binding fragment
157 FACS fluorescence-activated cell sorter
158 F-actin filamentous actin
159 FAD flavin-adenine dinucleotide
160 FAM 6-carboxyfluorescein
161 FBS fetal bovine serum
162 FBS Fetal bovine serum
163 Fc IgG fragment crystallizable
164 Fc-gamma R Receptor for the Fc-gamma part of the IgG molecule
165 FCM Flow cytometry
166 FcR Fc receptors (e.g., FcgRI)
167 FCS fetal calf serum
168 FISH fluorescence in situ hybridization
169 FITC fluorescein isothiocyanate
170 FLICE Fas-associated death domain-like IL-1b-converting enzyme
171 FLIP FLICE inhibitory protein
172 fMet formylmethionine
173 fMLP or FMLP formyl-methionyl-leucyl-phenylalanine
174 FMN flavin mononucleotide
175 FPLC fast protein liquid chromatography
176 Fru fructose
177 Fuc fucose
178 Fura 2-AM fura 2-acetoxymethyl ester
179 Fv IgG fragment variable
180 g gram (only with numbers)
181 G, Guo guanosine*
182 Gal galactose
183 GalN galactosamine
184 GALT gut-associated lymphoid tissue
185 GAPDH or G3PDH glyceraldehyde-3-phosphate dehydrogenase
186 GC, GLC gas chromatography, gas/liquid chromatography
187 G-CSF granulocyte CSF
188 GFP green fluorescent protein
189 Glc glucose
190 GlcA gluconic acid
191 GlcA, GlcUA glucuronic acid
192 GlcN glucosamine
193 GlcNAc N-acetylglucosamine
194 Gln glutamine
195 Glu glutamic acid
196 Glx glutamic acid or glutamine
197 Gly glycine
198 GM-CSF granulocyte-macrophage colony stimulating factor
199 gp glycoprotein (e.g., gp100)
200 GPI glycosylphosphatidylinositol
201 GST glutathione S-transferase
202 Gua guanine
203 GVH Graft-vs.-host (reaction)
204 h hour (only with numbers)
205 H chain heavy chain
206 H&E hematoxylin and eosin
207 HACA human anti-chimeric antibodies
208 HAHA human anti-human antibodies
209 HAMA human anti-mouse antibodies
210 Hb hemoglobin
211 HbCO carbon monoxide hemoglobin
212 HbO2 oxyhemoglobin
213 HBSS Hanks’ balanced salt solution
214 Hepes or HEPES N-2-hydroxyethylpiperazine-N’-2-ethanesulfonic acid
215 hf high frequency
216 hfs hyperfine structure
217 HHV human herpes virus
218 His histidine
219 HIV human immunodeficiency virus
220 HLA human leukocyte antigen
221 HPLC high-pressure or high-performance liquid chromatography
222 HPV human papillomavirus
223 HRP horseradish peroxidase
224 HSP Heat shock protein
225 HSV herpes simplex virus
226 Ht Height
227 HUVEC human umbilical vein endothelial cells
228 I, Ino inosine*
229 i.d. intradermal
230 i.d., o.d. diameter, inside or outside
231 i.m. intramuscular
232 i.p. intraperitoneal
233 i.v. intravenous
234 IC50 50% inhibition/inhibitory concentration
235 ICAM intercellular adhesion molecule
236 ICOS inducible costimulator
237 Id idiotope, idiotype
238 ID50 50% infective dose or 50% inhibiting dose
239 IDO indoleamine 2, 3-dioxygenase
240 IFA incomplete Freund’s adjuvant
241 IFN interferon (e.g., IFN-g)
242 Ig immunoglobulin
243 IgG, IgM, etc. immunoglobulin G, M, etc.
244 IgH Ig heavy chain
245 IkB inhibitory NF-kB
246 IL interleukin (e.g., IL-2)
247 Ile isoleucine
248 IMDM Iscove’s modified Dulbecco’s medium
249 IMEM Iscove’s minimal essential medium
250 IPTG isopropyl b-d-thiogalactoside
251 IR infrared
252 ITAM immunoreceptor tyrosine-based activation motif
253 ITIM immunoreceptor tyrosine-based inhibitory motif
254 IU international unit (only with numbers)
255 J region joining region of Ig or T cell receptor for Ag
256 JAK or Jak Janus kinase
257 JNK c-Jun N-terminal kinase
258 Ka association constant
259 kb kilobase (only with numbers)
260 kbp kilobase pair (only with numbers)
261 Kd distribution coefficient; dissociation constant
262 KD affinity constant
263 kDa kilodalton (only with numbers)
264 KIR Killer cell Ig-like receptor
265 L ligand
266 L chain light chain; light
267 LAK lymphokine-activated killer (cells)
268 LB Luria-Bertani or Lenox broth
269 LC Langerhans cell
270 LCMV Lymphocytic choriomeningitis virus
271 LD50 50% lethal dose
272 Leu leucine
273 LFA leukocyte (lymphocyte) function-associated Ag
274 LIF leukemia inhibitory factor
275 lim limit
276 LN Lymph node
277 LPS lipopolysaccharide
278 LTR long terminal repeat
279 LU lytic unit
280 Lys lysine
281 M molar (only with numbers)
282 m.p. melting point
283 m.w. molecular weight
284 mAb monoclonal antibody
285 MACS magnetic-activated cell sorting
286 MALDI matrix-assisted laser desorption ionization
287 MALDI-TOF matrix-assisted laser desorption ionization-time of flight
288 MALT mucosa-associated lymphoid tissue
289 Man mannose
290 MAPK mitogen-activated protein kinase
291 Mb myoglobin
292 MbCO carbon monoxide myoglobin
293 MCP-1 monocyte chemoattractant protein-1
294 M-CSF macrophage CSF
295 Me methyl
296 MEK mitogen-activated protein kinase kinase
297 MEM minimum essential medium
298 MES 2-(N-morpholino)ethanesulfonic acid
299 Met methionine
300 mg milligram (only with numbers)
301 MHC major histocompatibility complex
302 MIC Minimal inhibitory concentration
303 min minute (only with numbers)
304 MIP macrophage-inflammatory protein
305 ml milliliter (only with numbers)
306 MLC mixed lymphocyte culture
307 MLR mixed leukocyte reaction
308 mM millimolar (only with numbers)
309 mo month(s) (only with numbers)
310 mol mole
311 Mol wt Molecular weight
312 MOPS 4-morpholinepropanesulfonic acid
313 Mr relative molecular mass
314 MRI magnetic resonance imaging
315 mRNA messenger RNA
316 MS mass spectrometry or spectroscopy
317 mtDNA mitochondrial DNA
318 MTT 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide
319 MU Macrophage
320 MyD88 myeloid differentiating factor 88
321 n number in study or group
322 N, Nuc nucleoside (unknown)*
323 NAD nicotinamide adenine dinucleotide
324 NAD+ Nicotinamide adenine dinucleotide, oxidized
325 NADH Nicotinamide adenine dinucleotide, reduced
326 NaDodSO4 sodium dodecyl sulfate
327 NADP NAD phosphate
328 NADP+, NADPH nicotinamide-adenine dinucleotide phosphate
329 NADPH Nicotinamide adenine dinucleotide phosphate, reduced
330 NADPH+ Nicotinamide adenine dinucleotide phosphate, oxidized
331 NBT nitroblue tetrazolium
332 NCI National Cancer Institute
333 ND not determined
334 NDP nucleoside 5’-diphosphate
335 NF nuclear factor
336 NFAT or NF-AT nuclear factor of activated T cells
337 NF-kB nuclear factor kB
338 NIH National Institutes of Health
339 Ni-NTA nickel-nitrilotriacetic acid
340 NK natural killer (cells)
341 NKT Natural killer T (cell)
342 NMN nicotinamide mononucleotide
343 NMP nucleoside 5’-monophosphate
344 NMR nuclear magnetic resonance
345 NO nitric oxide
346 No. Number
347 NOD nonobese diabetic
348 NOESY nuclear Overhauser effect/enhancement spectroscopy
349 NP40 Nonidet-P40
350 NS not significant
351 nt nucleotide (only with numbers)
352 nt nucleotide (only with numbers)
353 OAc acetate
354 Obs., obs observed
355 OCT octamer-binding factor
356 OD optical density
357 oligo(dT), etc. Oligodeoxythymidylic acid, etc.
358 ORD optical rotatory dispersion
359 ORF open reading frame
360 OVA ovalbumin
361 p probability
362 P probability
363 P or p phosphate (in compounds)
364 PAGE polyacrylamide gel electrophoresis
365 PBL peripheral blood lymphocyte
366 PBMC peripheral blood mononuclear cell
367 PBS phosphate-buffered saline
368 PCR polymerase chain reaction
369 PCR-RFLP PCR-restriction fragment length polymorphism
370 PE phycoerythrin
371 PECAM-1 platelet endothelial cell adhesion molecule-1
372 PEG polyethylene glycol
373 PEI-cellulose polyethylenimine-cellulose
374 PerCP peridinin chlorophyll protein
375 PFC Plaque-forming cell
376 PFU or pfu plaque-forming unit
377 PG prostaglandin
378 Ph phenyl
379 PHA phytohemagglutinin
380 Phe phenylalanine
381 pI isoelectric point
382 Pi phosphate (inorganic)
383 pI isoelectric point
384 PI propidium iodide
385 PI3K phosphatidylinositol 3-kinase
386 PIPES piperazine-N
387 Pipes 1,4-piperazinediethanesulfonic acid
388 PK, PKC protein kinase, protein kinase C
389 PKC Protein kinase C
390 PMA phorbol myristate acetate
391 pmf proton-motive force
392 PMN Polymorphonuclear (cell, leukocyte)
393 PMSF phenylmethylsulfonyl fluoride or phenylmethanesulfonyl fluoride
394 poly(A), poly(dT), etc. Polyadenylic acid, polydeoxythymidylic acid, etc.
395 PPD Purified protein derivative of tuberculin
396 Pr propyl
397 Prepn Preparation
398 Pro proline
399 PWM pokeweed mitogen
400 QED quantum electrodynamics
401 r recombinant, (e.g., rIFN-g)
402 R receptor (e.g., IL-2R)
403 RACE rapid amplification of cDNA end
404 RAG recombination-activating gene
405 RANTES regulated upon activation
406 RBC red blood cell
407 rDNA, rRNA ribosomal DNA, ribosomal RNA
408 resp (mathematics) respectively
409 rf radio frequency
410 RFLP restriction fragment length polymorphism
411 RIA radioimmunoassay
412 Rib ribose
413 rms root-mean-square
414 RNA ribonucleic acid
415 RNase ribonuclease
416 rpm revolutions per minute
417 RPMI Roswell Park Memorial Institute (culture media)
418 rRNA ribosomal RNA
419 RT-PCR reverse transcriptase polymerase chain reaction
420 s second (only with numbers)
421 s.c. subcutaneous(ly)
422 SCID severe combined immunodeficiency
423 SD standard deviation
424 SDS sodium dodecyl sulfate
425 SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis
426 SE standard error
427 SEM standard error of the mean
428 Ser serine
429 SHIP src homology 2-containing inositol 5’ phosphatase
430 sIg Surface immunoglobulin
431 SIV simian immunodeficiency virus
432 SLE Systemic lupus erythematosus
433 SN Supernatant
434 Sp gr Specific gravity
435 sp. act. specific activity
436 SPF Specific pathogen free
437 SRBC sheep red blood cells
438 ss single-stranded (e.g., ssDNA)
439 SSC standard saline citrate
440 STAT signal transducer and activator of transcription
441 SV40 simian virus 40
442 T or Thd ribosylthymine
443 t1/2 half-life, half-time
444 TAMRA 5-(and 6)-carboxytetramethylrhodamine
445 TAP transporter associated with Ag processing
446 Tat terminal deoxynucleotidyltransferase
447 TBS Tris-buffered saline
448 TBST TBS with Tween 20
449 TCA trichloroacetic acid
450 TCR T cell receptor
451 TdR thymidine deoxyribose (also UdR, AdR)
452 TdT terminal deoxynucleotidyltransferase
453 Temp Temperature
454 TFA trifluoroacetic acid
455 Tg Transgenic
456 TGF transforming growth factor
457 Th T helper (cell)
458 Thr threonine
459 Thy thymine
460 TIL tumor-infiltrating lymphocyte
461 TLC thin-layer chromatography
462 TLR Toll-like receptor
463 TNF tumor necrosis factor
464 TNP trinitrophenyl
465 Tr Trace
466 TRAIL TNF-related apoptosis-inducing ligand
467 Tris tris(hydroxymethyl)aminomethane
468 tRNA transfer RNA
469 Trp tryptophan
470 TUNEL Tdt-mediated dUTP nick end labeling
471 Tyr tyrosine
472 U unit (only with numbers)
473 U, Urd uridine*
474 UHF ultrahigh frequency
475 Ura uracil
476 UTR untranslated region
477 UV ultraviolet
478 V region variable region of Ig
479 V(D)J variable diversity joining
480 v/v volume to volume ratio (%)
481 Val valine
482 VCAM vascular cell adhesion molecule
483 VLA very late activation Ag
484 vol volume
485 Vs Versus
486 VSV vesicular stomatitis virus
487 W watt (only with numbers)
488 WBC white blood cell
489 wk week (only with numbers)
490 WT wild type
491 Wt Weight
492 Xaa unknown or "other" amino acid
493 xid X-linked immunodeficiency
494 yr year (only with numbers)
495 ZAP70 ζ-associated protein 70 (or ζ-chain-associated protein 70)
496 μg microgram (only with numbers)
497 μl microliter (only with numbers)