test!Some test data for MIMOX!

Test Data Set (Download)

Less Critical Cases

Critical Cases


Abbreviations and explanations

Less critical cases are taken from case study of other existing tools. They might not be the best validation sets. However, we list them here to show our respect to the previous work by other researchers and to prove that MIMOX can reproduce the result from manual mapping and other existing tools such as FINDMAP and 3DEX. Critical cases are collected if they have both the structural epitope information and the mimotopes information.

*: Mapping result entry via MIMOX, which overlaps the native epitope;

TestSeq: (part or whole) sequence (or consensus) of mimotopes used for test; PDB: PDB structure of corresponding protein( the natural partner of selector); Selector: the material that was used to select the phage display library, it can be receptor or ligand, antibody or antigen, enzyme or substrate, cell, tissue, or even plastic...however, when used in epitope mapping, the selector should be antibody, especially monoclonal antibody.

ParaSet: a set of parameters used in a given MIMOX test. The ParaSet appears as " (Candidate residue pickup mode, Distance calculating method, Distance factor or threshold)".

Strict: pick up exactly the same residue as candidate residue; Similar: pick up the same and similar residues as candidate residues; CA: calculate distance between residues based on C alpha atoms; CB: calculate distance between residues based on C beta atoms; AHA: calculate distance between residues based on all heavy atoms. Distance factor (only valid for AHA method) ranges from 1.00 to 1.33 with a default value 1.11; Distance threshold (only valid for CA and CB methods) are 4.0Å~12.0Å with a default value 7.0Å.


Test 1

TestSeq: VPHPTWMR (Base on reference 12935344)
PDB: 1ATN_A  (Download)
Native Protein: actin
Selector: anti actin polyclonal antibody
Result from FINDMAP: VP(129,130)+HPT(101-103)+MW(355,356)+R372
Result from manually mapping by original author: VP(129,130)+HPT(101,102,358) +MW(355,356)+R372

Result from MIMOX:
ParaSet 1: (Strict, CA, 12.0); Select from Top26; Total: 184
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1 VAL-96--PRO-102--HIS-101--PRO-130--THR-358--TRP-356--MET-355--ARG-372 424.37
2 VAL-96--PRO-98--HIS-101--PRO-130--THR-358--TRP-356--MET-355--ARG-372 417.24
*5 VAL-129--PRO-130--HIS-101--PRO-102--THR-358--TRP-356--MET-355--ARG-372 405.56
*17 VAL-129--PRO-130--HIS-101--PRO-102--THR-103--TRP-356--MET-355--ARG-372 360.20
26 VAL-96--PRO-98--HIS-101--PRO-102--THR-103--TRP-356--MET-355--ARG-372 339.86


Test 2

TestSeq: FRYKII (virtually derived by the original authors)
PDB: 1QMC_A  (Download)
Selector: Fab fragment of mAb33
Native Protein: human immunodeficiency virus-1 integrase
Result from 3DEX: PHE 223|ARG 224|TYR 226|LYS 266|ILE 267|ILE 268
Result from docking result of original author:(F223,R224,Y226,K244,I267,I268)

Result from MIMOX:
ParaSet 1: (Strict, CA, 7.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1 PHE-223--ARG-224--TYR-226--LYS-266--ILE-267--ILE-268448.07
2 PHE-223--ARG-224--TYR-226--LYS-266--ILE-268--ILE-267 448.07


Test 3

TestSeq: LLTTNKD (Base on reference 15834923)
PDB: 1G9M_G  (Download)
Native Protein: HIV gp120 envelope glycoprotein
Selector: IgG from serum of HIV positive patients
Result from 3DEX: LEU 452|LEU 453|THR 283|THR 455|ASN 280|LYS 282|ASP 279

Result from MIMOX:
ParaSet 1: (Strict, CA, 7.0); Show Top3; Total: 5
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1 LEU-452--LEU-453--THR-283--THR-455--ASN-280--LYS-282--ASP-279265.82
2 LEU-452--LEU-454--THR-283--THR-455--ASN-280--LYS-282--ASP-279 265.39
3 LEU-259--LEU-453--THR-283--THR-455--ASN-280--LYS-282--ASP-279 264.96

ParaSet 2: (Similar, CA, 7.0); Show Top3; Total: 67
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1 ILE-360--ILE-467--SER-465--THR-358--ASN-356--LYS-357--GLU-464399.28
2 ILE-360--ILE-359--SER-465--THR-358--ASN-356--LYS-357--GLU-464 369.59
3 ILE-359--ILE-467--SER-465--THR-358--ASN-356--LYS-357--GLU-464 369.01

ParaSet 3: (Similar, AHA, 1.11); Show Top3; Total: 16
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1 LEU-86--VAL-85--THR-244--SER-243--ASN-229--LYS-231--GLU-267562.89
2 VAL-84--VAL-85--THR-244--SER-243--ASN-229--LYS-231--GLU-267 534.12
3 LEU-86--VAL-85--THR-244--SER-243--ASN-229--LYS-231--GLU-268 519.91

LLTTNKD IISTNKE LVTSNKE
Fig 1 :Comparing 3 Top1 from ParaSet 1, ParaSet 2 and ParaSet 3


Test 4 17b  (Download)

Mimotope sequences: 17bMimoSeq.fa (compiled from reference 14596802)

>17bMS1
SGLRNETFLR
>17bMS2
EFFQQHMLRVPR
>17bMS3
NMKLKLREMTQR
>17bMS4
MTRPTSLTQLTG
>17bMS5
LHIRVNETAYRV
>17bMS6
DFLREHGMKNPR
>17bMS7
RSRPTNMTTLRD
>17bMS8
AAYNATRGTVSA
>17bMS9
QLLHTWEDKMRK
>17bMS10
RNGELWLRRPGL
>17bMS11
MVRPSNWDALTR

Consensus Sequence: [LV]RP[LT][KR]LRE[LP][RT]X[-R]
TestSeq: LRLR

PDB: 1GC1_G
Selector: human mcAb 17b, Ig kappa
Native Protein: HIV gp120 envelope glycoprotein
Record in CED: CK(119,121)+VTQAC(200,202-205)+RKQI(419,421-423)+KMYP(432,434,435,437) ( CE0058 )
Result by Enshell-Seijffers method: LLKPCVKP(111,116-121,124)+VITQ-CPKV(200-208)+RIK-II(419-424)+KPP(432,437,438)

Result from MIMOX:
ParaSet 1: (Conservative, CA, 7.0); Show Top5; Total: 64
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1 ILE-423--LYS-421--ILE-420--ARG-419359.92
2ILE-491--LYS-490--VAL-489--LYS-487 345.35
3ILE-491--LYS-490--VAL-488--LYS-487342.39
*4VAL-200--LYS-121--LEU-122--LYS-432 315.78
*5ILE-423--LYS-432--LEU-122--LYS-121314.26


Test 5 trastuzumab  ( Download)

Mimotope sequences: HerceptinMimoSeq.fa (compiled from references 15210798 and 15829301)

Consensus Sequence: [KV][DL]Y[HW][AY][DE]--GEIT
TestSeq: KD, WAD, EGE

PDB: 1N8Z_C
Selector: humanized mouse mcAb, trastuzumab(Herceptin), IgG1 kappa
Native Protein: human receptor tyrosine-protein kinase erbB-2 (HER2)
Record in CED: PEADQ(557-561)+DPPF(570-573)+KFPDEEGACQP(593-603) ( CE0096 )

Result from MIMOX:
TestSeq: KD; ParaSet 1: (Strict, CA, 7.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1LYS-226--ASP-229157.92
2LYS-10--ASP-8150.23
3LYS-206--ASP-212123.97
4LYS-148--ASP-149 119.39
*5LYS-569--ASP-570109.39

TestSeq: WAD; ParaSet 1: (Conservative, CA, 7.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1PHE-573--ALA-559--GLU-558188.98
*2PHE-573--ALA-559--ASP-560153.76
3PHE-342--ALA-343--GLU-341143.86
4PHE-573--ALA-559--GLU-544 116.30

TestSeq: EGE; ParaSet 1: (Strict, CA, 7.0); Show Top3; Total: 6
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1GLU-597--GLY-599--GLU-598358.46
*2GLU-598--GLY-599--GLU-597 358.46
3GLU-481--GLY-484--GLU-485268.06


Test 6 82D6A3  ( Download)

Mimotope sequences: 82D6A3MimoSeq.fa (compiled from references 12855711)

Consensus Sequence: RT--[-FW]--[-LV]-SPWR
TestSeq: RT, FL, SPWR

PDB: 2ADF_A
Selector: mouse mcAb: 82D6A3, IgG
Native Protein: human von Willebrand factor (vWF)
Record in CED: ITTIDPWN(975-979,981-983) + DGFRY(1009,1012,1013,1016,1017) + MH(1022,1023) ( CE0154 )

Result from MIMOX:
TestSeq: RT; ParaSet 1: (Strict, CA, 7.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1ARG-1056--THR-1058270.62
*2ARG-1016--THR-1019 178.19
3ARG-1067--THR-1038139.97

TestSeq: FL; ParaSet 1: (Conservative, CA, 7.0); Show Top2; Total: 16
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1PHE-1013--VAL-101576.08
*2PHE-1013--LEU-101168.87

TestSeq: SPWR; ParaSet 1: (Conservative, CA, 10.0); Select from Top14; Total: 31
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1SER-942--PRO-940--PHE-939--ARG-1067330.44
2SER-937--PRO-940--PHE-939--ARG-1067327.04
*14THR-977--PRO-981--TRP-982--ARG-1026165.95


Test 7 13b5  (Download)

Mimotope sequences: 13b5MimoSeq.fa (compiled from reference 14596802)

Consensus Sequence: [DE]V[FM]GPL[STDE]TX-X[DE]
TestSeq: GPL, ET, EE (EE is formed by 2 ends because of CC type of phage displayed peptides)

PDB: 1E6J_P
Selector: mouse mab 13B5, IgG1 kappa
Native Protein: HIV-1 Capsid protein p24
Record in CED: ALGPAATEE(204-210,212,213)+TA(216-217) ( CE0170 )
Result by Enshell-Seijffers method: E187+D197+A204+GPAA(206-209)+EE(212-213)+A217

Result from MIMOX:
TestSeq: GPL; ParaSet 1: (Strict, CA, 8.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1GLY-206--PRO-207--LEU-205250.24
2GLY-106--PRO-49--LEU-52 20.41
3GLY-127--PRO-49--LEU2.29

TestSeq: ET; ParaSet 1: (Strict, CA, 7.0); Show Top3; Total: 11
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1GLU-212--THR-216200.95
*2GLU-213--THR-216 182.45
*3GLU-212--THR-210181.88

TestSeq: EE; ParaSet 1: (Conservative, CA, 7.0); Show Top3; Total: 18
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1GLU-28--GLU-29254.99
2GLU-29--GLU-28 254.99
*3GLU-212--GLU-213207.22


Test 8 BO2C11  (Download)

Mimotope sequences: BO2C11MimoSeq.fa (compiled from reference 12676786)

Consensus Sequence: [NQKR][HST]RWSNRSS[ST]
TestSeq: QH, RWSN, RSSS

PDB: 1IQD_C
Selector: human mcAb,BO2C11, IgG4 kappa
Native Protein: human coagulation factor VIII
Record in CED: FTNMF(2196-2200)+R2215+RPQV(2220-2223)+SLLT(2250-2253)+HQ(2315-2316) ( CE0176 )

Result of MIMOP-MimAlign:
SS(2193-2194)+NM(2198-2199)+T2202+RR(2215,2220)+L2252+SQDF(2254,2287-2290)+HQSWH(2309,2311-2315)
Result of MIMOP-MimCons:
TSSY(2191,2193-2195)+R2220+NNPKW(2224-2227,2229)+RHQ(2307,2309,2311)
Result of combined: YFTNMFTKRRQ(2195-2200,2202,2207,2215,2220,2222)

Result from MIMOX:
TestSeq: QH; ParaSet 1: (Conservative, CA, 7.0); Show all
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1GLN-2270--HIS-2269285.38
2GLN-2213--HIS-2211 217.84
*3GLN-2316--HIS-2315170.19
4GLN-2311--HIS-2309 87.88

TestSeq: RWSN; ParaSet 1: (Conservative, CA, 7.0); Show Top3; Total: 11
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1LYS-2281--PHE-2274--THR-2272--GLN-2270265.10
2LYS-2207--TRP-2203--THR-2197--ASN-2198 235.32
*3ARG-2220--PHE-2196--THR-2197--ASN-2198234.17

TestSeq: RSSS; ParaSet 1: (Conservative, CA, 7.0); Show Top3; Total: 51
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1ARG-2215--SER-2216--THR-2202--THR-2197311.80
*2ARG-2215--SER-2216--THR-2202--SER-2204262.39
*3LYS-2249--SER-2250--SER-2254--THR-2253246.28


Test 9 C225 (cetuximab)  ( Download)

Mimotope sequences: C225MimoSeq.fa (compiled from reference 16288119)

Consensus Sequence: QW[DNQ][LR][SFW]SRX[LY]K
TestSeq: QWQ, LSSR

PDB: 1YY9_A
Selector: humanized mouse mcAb: c225(cetuximab, Erbitux), IgG1 kappa
Native Protein: human epidermal growth factor receptor (EGFR)
Record in CED: R353+Q384+QHFVS(408-409,412,417-418)+ISK(438,440,443)+KIISN(465-468,473) ( CE0199 )

Result from MIMOX:
TestSeq: QWQ; ParaSet 1: (Conservative, CA, 7.0); Select from Top7; Total: 18
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
1ASN-32--PHE-54--ASN-33199.73
*7GLN-408--PHE-412--GLN-411 163.34

TestSeq: LSSR; ParaSet 1: (Conservative, CA, 7.0); Show Top5; Total: 87
NoResidues and Locations of Candidate Cluster Accessibility (Å2)
*1ILE-467--SER-440--SER-468--LYS-443338.65
2VAL-526--SER-529--SER-506--ARG-509333.02
3VAL-312--SER-342--THR-378--ARG-405316.79
*4VAL-417--SER-440--SER-468--LYS-443308.62
*5ILE-466--SER-440--SER-468--LYS-443295.59



HLAB | Center of Bioinformatics | UESTC | Chengdu, 610054, China  [Feedback]