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PMC:7245302 / 35844-39156 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
365 2960-2964 Gene denotes TLR3 Gene:7098
367 3163-3167 Gene denotes TLR4 Gene:7099
396 121-125 Gene denotes TLR3 Gene:7098
397 130-134 Gene denotes TLR4 Gene:7099
398 220-224 Gene denotes TLR3 Gene:7098
399 229-233 Gene denotes TLR4 Gene:7099
400 351-356 Gene denotes NF-κB Gene:4790
401 814-818 Gene denotes TLR3 Gene:7098
402 2218-2222 Gene denotes TLR4 Gene:7099
403 1654-1662 Chemical denotes hydrogen MESH:D006859
404 2730-2735 Chemical denotes Pro23
405 2737-2742 Chemical denotes Glu24
406 2744-2749 Chemical denotes Ser25
407 2751-2756 Chemical denotes Asp44
408 2758-2763 Chemical denotes Lys47
409 2765-2770 Chemical denotes Asp50
410 2772-2777 Chemical denotes Asp51
411 2779-2784 Chemical denotes Arg67
412 2786-2791 Chemical denotes Arg87
413 2793-2798 Chemical denotes Glu89
414 2800-2806 Chemical denotes Pro113
415 2808-2814 Chemical denotes Gln115
416 2816-2822 Chemical denotes Asp137
417 2824-2830 Chemical denotes His159
418 2832-2838 Chemical denotes Asp160
419 2840-2846 Chemical denotes Ser184
420 2852-2858 Chemical denotes Lys186
421 2881-2886 Chemical denotes Lys20
422 2888-2893 Chemical denotes Phe64
423 2899-2905 Chemical denotes Asp114

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T178 181-188 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T179 396-405 Body_part denotes cytokines http://purl.org/sig/ont/fma/fma84050
T180 1382-1386 Body_part denotes body http://purl.org/sig/ont/fma/fma256135

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T253 179-180 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 189-196 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T255 318-326 http://purl.obolibrary.org/obo/CLO_0001658 denotes activate
T256 341-350 http://purl.obolibrary.org/obo/SO_0000418 denotes signaling
T257 355-356 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T258 589-599 http://purl.obolibrary.org/obo/CLO_0001658 denotes activation
T259 950-951 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T260 1669-1671 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T261 1763-1764 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T262 2453-2455 http://purl.obolibrary.org/obo/CLO_0003622 denotes HB
T263 2664-2665 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T264 2718-2719 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T265 3000-3007 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T266 3203-3210 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T218 181-188 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T219 189-196 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T220 351-353 Chemical denotes NF http://purl.obolibrary.org/obo/CHEBI_141424|http://purl.obolibrary.org/obo/CHEBI_25573|http://purl.obolibrary.org/obo/CHEBI_1224
T223 567-577 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T224 703-711 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T225 1008-1017 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T226 1055-1064 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T227 1212-1221 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T228 1435-1443 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T229 1654-1662 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T230 1856-1864 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T231 2246-2254 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T47 135-148 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immune
T48 341-350 http://purl.obolibrary.org/obo/GO_0023052 denotes signaling
T49 451-466 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immunity
T50 615-632 http://purl.obolibrary.org/obo/GO_0006952 denotes defense responses
T51 772-785 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immune
T52 2965-2978 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immune
T53 3168-3181 http://purl.obolibrary.org/obo/GO_0045087 denotes innate immune

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T270 0-45 Sentence denotes 3.9 MEPVC Interactions with Immune Receptors
T271 46-214 Sentence denotes Molecular interactions and binding conformation of the designed MEPVC with TLR3 and TLR4 innate immune receptors were deciphered via a protein-peptide docking approach.
T272 215-475 Sentence denotes Both TLR3 and TLR4 belong to toll-like receptor family of pattern recognition receptor and function to activate intracellular signaling NF-κB pathway and production of inflammatory cytokines responsible for the development of effective innate immunity [79,80].
T273 476-633 Sentence denotes These receptors recognize viral associated molecular patterns and induce the production of interferon leading to activation of strong host defense responses.
T274 634-796 Sentence denotes Also, the specific adaptive immunity takes time to establish against antigens therefore it's important to evaluate MEPVC affinity for the innate immune receptors.
T275 797-949 Sentence denotes In case of MRPVC-TLR3 complex, the patch dock predicted 10 best solutions sorted based on the docking geometric shape complementarity score (S-Table 3).
T276 950-1092 Sentence denotes A high score implies enhanced affinity of the interacting molecules and best docked conformations of the molecules with respect to each other.
T277 1093-1222 Sentence denotes Solution 3 was visualized for docked conformations and intermolecular forces responsible for such high affinity of the molecules.
T278 1223-1405 Sentence denotes The selection was based on the FireDock analysis (S-Table 4) which is an efficient package for refinement and reassigning procedure of docking scores to rigid body docking solutions.
T279 1406-1518 Sentence denotes The global binding energy of solution 3 is better i.e. -6.39 kJ/mol compared to the rest of predicted solutions.
T280 1519-1742 Sentence denotes The contribution to the total score form attractive van der Waals (VdW) energy is -12.12 kJ/mol, repulsive (VdW) energy (4.79 kJ/mol), hydrogen bond (HB) energy (-1.63 kJ/mol), and atomic contact energy (ACE) (5.95 kJ/mol).
T281 1743-2181 Sentence denotes The MEPVC, within 3 Å, was noticed to posed right in the center of the TLR3 receptor (Figure 7 ) interacting via hydrogen and hydrophobic bonds with His156, Asp180, Lys201, Glu203, Ser206, Phe227, Asp229, Asp230, Ser254, Ser256, Asp257, Ser282, Tyr283, Asp284, Asp285, Glu301, Tyr302, Phe304, Glu306, Tyr307, Arg325, Glu358, His359, Lys382, Tyr383, P408, His410, Iso411, Gly431, His432, Glu434, Pro408, Asp457, Phe459, Gln483, and Glu533.
T282 2182-2417 Sentence denotes Similarly, among 10 predicted MEPVC-TLR4 complexes (S-Table 5), solution 7 (S-Table 6) was affirmed as best with total global energy of -10.39 kJ/mol whereas the rest of complexes were noticed as highly unstable with score in positive.
T283 2418-2575 Sentence denotes The attractive VdW, repulsive VdW, HB and ACE contribution to the global energy is -35.75 kJ/mol, 22.04 kJ/mol, -5.51 kJ/mol, and 12.61 kJ/mol, respectively.
T284 2576-2684 Sentence denotes Visual analysis of the complex revealed binding of the MEPVC at the interface of chains B and D (Figure 8 ).
T285 2685-2729 Sentence denotes The MEPVC is surrounded by chain B residues:
T286 2730-2880 Sentence denotes Pro23, Glu24, Ser25, Asp44, Lys47, Asp50, Asp51, Arg67, Arg87, Glu89, Pro113, Gln115, Asp137, His159, Asp160, Ser184, and Lys186 and chain D residues:
T287 2881-2906 Sentence denotes Lys20, Phe64, and Asp114.
T288 2907-2988 Sentence denotes Fig. 7 Binding conformation of MEPVC with respect to TLR3 innate immune receptor.
T289 2989-3109 Sentence denotes The yellow labeled region pointing to the residues involved in both hydrophobic and hydrophilic interactions with MEPVC.
T290 3110-3191 Sentence denotes Fig. 8 Binding conformation of MEPVC with respect to TLR4 innate immune receptor.
T291 3192-3312 Sentence denotes The yellow labeled region pointing to the residues involved in both hydrophobic and hydrophilic interactions with MEPVC.

2_test

Id Subject Object Predicate Lexical cue
32454128-25071777-29238342 468-470 25071777 denotes 79
32454128-27162029-29238343 471-473 27162029 denotes 80

MyTest

Id Subject Object Predicate Lexical cue
32454128-25071777-29238342 468-470 25071777 denotes 79
32454128-27162029-29238343 471-473 27162029 denotes 80