Testing machine learning techniques for general application by using protein secondary structure prediction. A brief survey with studies of pitfalls and benefits using a simple progressive learning approach
Many researchers have just lately used the prediction of protein secondary construction (native conformational states of amino acid residues) to check advances in predictive and machine studying know-how equivalent to Neural Web Deep Studying.
Protein secondary construction prediction continues to be a useful instrument in analysis in biomedicine and the life sciences, however it is usually extraordinarily attractive for testing predictive strategies equivalent to neural nets which are meant for various or extra normal functions. A complication is highlighted right here for researchers testing their strategies for different functions.
Trendy protein databases inevitably include necessary clues to the reply, so-called “sturdy buried clues”, although usually obscurely; they’re onerous to keep away from. It’s because most proteins or components of proteins in a contemporary protein knowledge base are associated to others by organic evolution.
For researchers creating machine studying and predictive strategies, this will overstate and so confuse understanding of the true high quality of a predictive technique. Nonetheless, for researchers utilizing the algorithms as instruments, understanding sturdy buried clues is of nice worth, as a result of they should make most use of all data obtainable.
A easy technique associated to the GOR strategies however with some options of neural nets within the sense of progressive studying of huge numbers of weights, is used to discover this. It may well purchase tens of hundreds of thousands and therefore gigabytes of weights, however they’re realized stably by exhaustive sampling. The importance of the findings is mentioned within the mild of promising latest outcomes from AlphaFold utilizing Google’s DeepMind.
Predicted Construction of Totally Activated Tas1R3/1R3′ Homodimer Certain to G Protein and Pure Sugars: Structural Insights into G Protein Activation by a Class C Candy Style Homodimer with Pure Sugars
The Tas1R3 G protein-coupled receptor constitutes the principle element of candy style sensory response in people through forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3′ homodimer serves as a low-affinity candy style receptor, stimulating gustducin G protein (GGust) signaling within the presence of a excessive focus of pure sugars.
This gives a further means to detect the style of pure sugars, thereby differentiating the flavors between pure sugars and synthetic sweeteners. We report right here the expected 3D construction of energetic state Tas1R3/1R3′ homodimer complexed with heterotrimeric GGust and sucrose.
We found that the GGust makes ionic anchors to intracellular loops 1 and a pair of of Tas1R3 whereas the Gα-α5 helix engages the cytoplasmic area extensively by way of salt bridge and hydrophobic interactions. We present that within the activation of this advanced the Venus flytrap domains of the homodimer bear a exceptional twist as much as ∼100° rotation across the vertical axis to undertake a closed-closed conformation whereas the intracellular area relaxes to an open-open conformation.
We discover that binding of sucrose to the homodimer stabilizes a preactivated conformation with a largely open intracellular area that recruits and prompts the GGust. Upon activation, the Gα subunit spontaneously opens up the nucleotide-binding web site, making nucleotide trade facile for signaling.
This activation of GGust promotes the interdomain twist of the Venus flytrap domains. These constructions and transformations may probably be a foundation for the design of latest sweeteners with larger exercise and fewer disagreeable flavors.
A novel lncRNA-protein interplay prediction technique based mostly on deep forest with cascade forest construction
Lengthy noncoding RNAs (lncRNAs) regulate many organic processes by interacting with corresponding RNA-binding proteins. The identification of lncRNA-protein Interactions (LPIs) is considerably necessary to properly characterize the organic features and mechanisms of lncRNAs. Present computational strategies have been successfully utilized to LPI prediction.
Nonetheless, the vast majority of them had been evaluated solely on one LPI dataset, thereby leading to prediction bias. Extra importantly, a part of fashions didn’t uncover doable LPIs for brand new lncRNAs (or proteins). As well as, the prediction efficiency stays restricted. To unravel with the above issues, on this research, we develop a Deep Forest-based LPI prediction technique (LPIDF).
First, 5 LPI datasets are obtained and the corresponding sequence data of lncRNAs and proteins are collected. Second, options of lncRNAs and proteins are constructed based mostly on four-nucleotide composition and BioSeq2vec with encoder-decoder construction, respectively.
Lastly, a deep forest mannequin with cascade forest construction is developed to seek out new LPIs. We evaluate LPIDF with 4 classical affiliation prediction fashions based mostly on three fivefold cross validations on lncRNAs, proteins, and LPIs.
LPIDF obtains higher common AUCs of 0.9012, 0.6937 and 0.9457, and the perfect common AUPRs of 0.9022, 0.6860, and 0.9382, respectively, for the three CVs, considerably outperforming different strategies. The outcomes present that the lncRNA FTX could work together with the protein P35637 and wishes additional validation.
Construction, Exercise and Perform of the MLL2 (KMT2B) Protein Lysine Methyltransferase
The Blended Lineage Leukemia 2 (MLL2) protein, also referred to as KMT2B, belongs to the household of mammalian histone H3 lysine 4 (H3K4) methyltransferases. It’s a giant protein of 2715 amino acids, broadly expressed in grownup human tissues and a paralog of the MLL1 protein.
MLL2 accommodates a attribute C-terminal SET area answerable for methyltransferase exercise and kinds a protein advanced with WRAD (WDR5, RbBP5, ASH2L and DPY30), host cell components half (HCF half) and Menin. The MLL2 advanced is answerable for H3K4 trimethylation (H3K4me3) on particular gene promoters and close by cis-regulatory websites, regulating bivalent developmental genes in addition to stem cell and germinal cell differentiation gene units.
Furthermore, MLL2 performs a important function in improvement and germ line deletions of Mll2 have been related to early progress retardation, neural tube defects and apoptosis that results in embryonic dying. It has additionally been concerned within the management of voluntary motion and the pathogenesis of early stage childhood dystonia.
Moreover, tumor-promoting features of MLL2 have been detected in a number of most cancers sorts, together with colorectal, hepatocellular, follicular most cancers and gliomas. On this evaluation, we talk about the principle structural and practical elements of the MLL2 methyltransferase with explicit emphasis on transcriptional mechanisms, gene regulation and affiliation with ailments.
Molecular hybrids: A five-year survey on constructions of a number of focused hybrids of protein kinase inhibitors for most cancers remedy
Protein kinases have grown over the previous few years as an important goal for various most cancers sorts. With the multifactorial nature of most cancers, and the quick improvement of drug resistance for standard chemotherapeutics, a method for designing multi-target brokers was advised to probably improve drug efficacy, reduce unwanted effects and retain the right pharmacokinetic properties.
Kinase inhibitors had been used extensively in such technique. Totally different kinase inhibitor brokers which goal EGFR, VEGFR, c-Met, CDK, PDK and different targets had been merged into hybrids with standard chemotherapeutics equivalent to tubulin polymerization and topoisomerase inhibitors. Different hybrids had been designed gathering kinase inhibitors with focused most cancers remedy equivalent to HDAC, PARP, HSP 90 inhibitors.
) Recombinant E.Coli Dnak (HSP70) |
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| 7-06944 | CHI Scientific | 50µg | Ask for price |
Recombinant E.Coli Dnak (HSP70) |
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| 7-06945 | CHI Scientific | 1mg | Ask for price |
) Recombinant E.Coli Dnak (HSP70) |
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| RP-615 | Alpha Diagnostics | 20 ug | EUR 164 |
 Human Heat Shock Protein 90 alpha (hsp90/hsp90 alpha/dnak) protein control for Western) Recombinant (E.Coli) Human Heat Shock Protein 90 alpha (hsp90/hsp90 alpha/dnak) protein control for Western |
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| HSP903-C | Alpha Diagnostics | 100ul | EUR 286 |
 Antibody) Chaperone Protein DnaK (DNAK) Antibody |
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| 20-abx300649 | Abbexa |
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 Dnak protein |
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| 30R-1019 | Fitzgerald | 100 ug | EUR 224 |
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Description: Purified recombinant E.coli Dnak protein |
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Dnak protein |
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| 30R-1020 | Fitzgerald | 100 ug | EUR 224 |
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Description: Purified recombinant E.coli Dnak protein |
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Dnak protein |
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| 30R-1021 | Fitzgerald | 100 ug | EUR 224 |
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Description: Purified recombinant E.coli Dnak protein |
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Dnak protein |
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| 30R-1022 | Fitzgerald | 100 ug | EUR 224 |
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Description: Purified recombinant E.coli Dnak protein |
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Dnak protein |
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| 30R-1023 | Fitzgerald | 100 ug | EUR 224 |
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Description: Purified recombinant E.coli Dnak protein |
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 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-100ug |
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| QP7629-ec-100ug | EnQuireBio | 100ug | EUR 707 |
 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-10ug |
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| QP7629-ec-10ug | EnQuireBio | 10ug | EUR 326 |
 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-1mg |
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| QP7629-ec-1mg | EnQuireBio | 1mg | EUR 2303 |
 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-200ug |
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| QP7629-ec-200ug | EnQuireBio | 200ug | EUR 1115 |
 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-500ug |
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| QP7629-ec-500ug | EnQuireBio | 500ug | EUR 1514 |
 Recombinant E.coli Chaperone protein DnaK Protein, His, E.coli-50ug |
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| QP7629-ec-50ug | EnQuireBio | 50ug | EUR 435 |
) Escherichia coli Chaperone protein DnaK (dnaK) |
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| 1-CSB-YP633459EGW | Cusabio |
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Description: Recombinant Escherichia coli Chaperone protein DnaK(dnaK) expressed in Yeast |
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) Mycoplasma pneumoniae Chaperone protein DnaK (dnaK) |
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| 1-CSB-EP301110MLW | Cusabio |
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Description: Recombinant Mycoplasma pneumoniae Chaperone protein DnaK(dnaK) ,partial expressed in E.coli |
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Escherichia coli Chaperone protein DnaK (dnaK) |
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| 1-CSB-EP633459EGW | Cusabio |
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Description: Recombinant Escherichia coli Chaperone protein DnaK(dnaK) expressed in E.coli |
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 Antibody (HRP)) Chaperone Protein DnaK (DNAK) Antibody (HRP) |
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| 20-abx300799 | Abbexa |
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 Antibody (FITC)) Chaperone Protein DnaK (DNAK) Antibody (FITC) |
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| 20-abx300800 | Abbexa |
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 Antibody (Biotin)) Chaperone Protein DnaK (DNAK) Antibody (Biotin) |
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| 20-abx300801 | Abbexa |
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 Recombinant E.Coli Dnak Substrate Binding Domain C-terminal |
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| 7-06949 | CHI Scientific | 20µg | Ask for price |
Recombinant E.Coli Dnak Substrate Binding Domain C-terminal |
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| 7-06950 | CHI Scientific | 100µg | Ask for price |
Recombinant E.Coli Dnak Substrate Binding Domain C-terminal |
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| 7-06951 | CHI Scientific | 1mg | Ask for price |
 Dnak Substrate Binding Domain C-terminal) Recombinant (E.Coli) Dnak Substrate Binding Domain C-terminal |
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| RP-618 | Alpha Diagnostics | 20 ug | EUR 164 |
 Recombinant other DnaK Protein, Untagged, E.coli-10ug |
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| QP11682-10ug | EnQuireBio | 10ug | EUR 155 |
 Recombinant other DnaK Protein, Untagged, E.coli-1mg |
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| QP11682-1mg | EnQuireBio | 1mg | EUR 1859 |
 Recombinant other DnaK Protein, Untagged, E.coli-50ug |
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| QP11682-50ug | EnQuireBio | 50ug | EUR 201 |
 Recombinant Human DnaK Protein, His, E.coli-10ug |
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| QP11683-10ug | EnQuireBio | 10ug | EUR 155 |
 Recombinant Human DnaK Protein, His, E.coli-1mg |
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| QP11683-1mg | EnQuireBio | 1mg | EUR 1959 |
 Recombinant Human DnaK Protein, His, E.coli-50ug |
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| QP11683-50ug | EnQuireBio | 50ug | EUR 201 |
) Cyanophora paradoxa Chaperone protein dnaK (dnaK-A) |
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| 1-CSB-EP656399DZX | Cusabio |
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Description: Recombinant Cyanophora paradoxa Chaperone protein dnaK(dnaK-A),partial expressed in E.coli |
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 Recombinant E.Coli Dnak Substrate Binding Domain |
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| 7-06946 | CHI Scientific | 20µg | Ask for price |
Recombinant E.Coli Dnak Substrate Binding Domain |
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| 7-06947 | CHI Scientific | 100µg | Ask for price |
Recombinant E.Coli Dnak Substrate Binding Domain |
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| 7-06948 | CHI Scientific | 1mg | Ask for price |
 Recombinant E.Coli Dnak ATPase Binding Domain |
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| 7-06952 | CHI Scientific | 10µg | Ask for price |
Recombinant E.Coli Dnak ATPase Binding Domain |
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| 7-06953 | CHI Scientific | 50µg | Ask for price |
Recombinant E.Coli Dnak ATPase Binding Domain |
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| 7-06954 | CHI Scientific | 1mg | Ask for price |
 Recombinant E.Coli Dnak Lid Covering Substrate |
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| 7-06955 | CHI Scientific | 20µg | Ask for price |
Recombinant E.Coli Dnak Lid Covering Substrate |
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| 7-06956 | CHI Scientific | 100µg | Ask for price |
Recombinant E.Coli Dnak Lid Covering Substrate |
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| 7-06957 | CHI Scientific | 1mg | Ask for price |
 Dnak Substrate Binding Domain) Recombinant (E.Coli) Dnak Substrate Binding Domain |
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| RP-617 | Alpha Diagnostics | 20 ug | EUR 164 |
 Dnak ATPase Binding Domain) Recombinant (E.Coli) Dnak ATPase Binding Domain |
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| RP-619 | Alpha Diagnostics | 20 ug | EUR 164 |
 Dnak Lid Covering Substrate) Recombinant (E.Coli) Dnak Lid Covering Substrate |
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| RP-620 | Alpha Diagnostics | 20 ug | EUR 164 |
 Protein) Dnak (HSP70) Protein |
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| 20-abx260416 | Abbexa |
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Dnak (HSP70) Protein |
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| 20-abx260492 | Abbexa |
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 control for Western) Recombinant purified M. tuberculosis Heat Shock Protein 70 (hsp70/hsp72/Dnak/ML2496) control for Western |
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| HSP701-C | Alpha Diagnostics | 100 ul | EUR 286 |
 dnaK Antibody |
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| 1-CSB-PA633459HA01EGW | Cusabio |
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Description: A polyclonal antibody against dnaK. Recognizes dnaK from Escherichia coli. This antibody is Unconjugated. Tested in the following application: ELISA, WB; Recommended dilution: WB:1:500-1:5000 |
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 Recombinant other DnaK ATPase-BD Protein, Untagged, E.coli-10ug |
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| QP11684-10ug | EnQuireBio | 10ug | EUR 155 |
 Recombinant other DnaK ATPase-BD Protein, Untagged, E.coli-1mg |
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| QP11684-1mg | EnQuireBio | 1mg | EUR 1859 |
 Recombinant other DnaK ATPase-BD Protein, Untagged, E.coli-50ug |
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| QP11684-50ug | EnQuireBio | 50ug | EUR 201 |
 Recombinant other DnaK Mycobacterium Tuberculosis Protein, Untagged, E.coli-100ug |
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| QP11686-100ug | EnQuireBio | 100ug | EUR 1315 |
 Recombinant other DnaK Mycobacterium Tuberculosis Protein, Untagged, E.coli-10ug |
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| QP11686-10ug | EnQuireBio | 10ug | EUR 201 |
 Recombinant other DnaK Mycobacterium Tuberculosis Protein, Untagged, E.coli-2ug |
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| QP11686-2ug | EnQuireBio | 2ug | EUR 155 |
 Dnak Substrate Binding Domain C-terminal Protein |
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| 20-abx263150 | Abbexa |
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 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-100ug |
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| QP6942-ec-100ug | EnQuireBio | 100ug | EUR 707 |
 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-10ug |
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| QP6942-ec-10ug | EnQuireBio | 10ug | EUR 326 |
 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-1mg |
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| QP6942-ec-1mg | EnQuireBio | 1mg | EUR 2303 |
 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-200ug |
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| QP6942-ec-200ug | EnQuireBio | 200ug | EUR 1115 |
 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-500ug |
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| QP6942-ec-500ug | EnQuireBio | 500ug | EUR 1514 |
 Recombinant Mycoplasma Chaperone protein DnaK Protein, His-SUMO, E.coli-50ug |
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| QP6942-ec-50ug | EnQuireBio | 50ug | EUR 435 |
 SHANK1a C-terminus |
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| RA19016 | Neuromics | 100 ug | EUR 344 |
 C. perfringens alpha toxin protein control for western blot) Recombinant (E.coli) C. perfringens alpha toxin protein control for western blot |
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| CPA11-C | Alpha Diagnostics | 100 ul | EUR 286 |
 C. perfringens beta toxin protein control for western blot) Recombinant (E.coli) C. perfringens beta toxin protein control for western blot |
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| CPB12-C | Alpha Diagnostics | 100 ul | EUR 286 |
 C. perfringens epsilon toxin protein control for western blot) Recombinant (E.coli) C. perfringens epsilon toxin protein control for western blot |
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| CPE13-C | Alpha Diagnostics | 100 ul | EUR 286 |
 Recombinant other DnaK Lid Covering Subst Protein, Untagged, E.coli-100ug |
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| QP11685-100ug | EnQuireBio | 100ug | EUR 201 |
 Recombinant other DnaK Lid Covering Subst Protein, Untagged, E.coli-1mg |
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| QP11685-1mg | EnQuireBio | 1mg | EUR 1061 |
 Recombinant other DnaK Lid Covering Subst Protein, Untagged, E.coli-20ug |
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| QP11685-20ug | EnQuireBio | 20ug | EUR 155 |
 Recombinant Mycobacterium Tuberculosis dnaK Protein |
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| VAng-Yyj0039-inquire | Creative Biolabs | inquire | Ask for price |
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Description: Mycobacterium Tuberculosis Chaperone protein DnaK (dnaK), recombinant protein. |
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 Recombinant Bacillus Thermoglucosidasius dnaK Protein |
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| VAng-Lsx1545-inquire | Creative Biolabs | inquire | Ask for price |
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Description: Bacillus thermoglucosidasius Chaperone protein DnaK, recombinant protein. |
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 Recombinant Aeromonas Hydrophila dnaK Protein |
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| VAng-Lsx0879-inquire | Creative Biolabs | inquire | Ask for price |
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Description: Aeromonas Hydrophila Chaperone protein DnaK, recombinant protein. |
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 Recombinant Aeromonas Salmonicida dnaK Protein |
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| VAng-Lsx1239-inquire | Creative Biolabs | inquire | Ask for price |
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Description: Aeromonas Salmonicida Chaperone protein DnaK, recombinant protein. |
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 Dnak ATPase Binding Domain Protein |
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| 20-abx260417 | Abbexa |
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 Dnak Substrate Binding Domain Protein |
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| 20-abx263149 | Abbexa |
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 Dnak Lid Covering Substrate Protein |
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| 20-abx263151 | Abbexa |
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 Protein) Myobacterium Tuberculosis DnaK (HSP70) Protein |
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| 20-abx263478 | Abbexa |
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) Aldolase C (C-terminus Specific) |
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| MO22157 | Neuromics | 100 ul | EUR 435 |
) Ret (C-Terminus Fused) |
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| MO15089 | Neuromics | 500 ug | EUR 910 |
 CTGF/CCN2 C-Terminus |
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| MO15139 | Neuromics | 100 ug | EUR 492 |
) VR1 C-terminus (TRPV1) |
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| P14100 | Neuromics | 100 ug Blocking Peptide | EUR 146 |
VR1 C-terminus (TRPV1) |
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| GP14100 | Neuromics | 50 ul | EUR 268 |
) FOXO1 antibody (C-terminus) |
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| 10R-10726 | Fitzgerald | 100 ug | EUR 381 |
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Description: Mouse monoclonal FOXO1 antibody (C-terminus) |
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) GRP78 antibody (C-terminus) |
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| 10R-10756 | Fitzgerald | 100 ug | EUR 381 |
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Description: Mouse monoclonal GRP78 antibody (C-terminus) |
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) COX4 antibody (C-terminus) |
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| 10R-10795 | Fitzgerald | 100 ug | EUR 381 |
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Description: Mouse monoclonal COX4 antibody (C-terminus) |
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) AMACR antibody (C-terminus) |
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| 10R-10812 | Fitzgerald | 100 ug | EUR 381 |
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Description: Mouse monoclonal AMACR antibody (C-terminus) |
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 Mycobacterium Tuberculosis Recombinant Protein) DnaK (HSP70) Mycobacterium Tuberculosis Recombinant Protein |
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| PROTP19993 | BosterBio | Regular: 10ug | EUR 317 |
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Description: Recombinant Mycobacterium Tuberculosis Dnak produced in E.Coli is a single, non-glycosylated polypeptide chain containing 625 amino acids and having a molecular mass of 66.7 kDa. |
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 dnaK Antibody, HRP conjugated |
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| 1-CSB-PA633459HB01EGW | Cusabio |
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Description: A polyclonal antibody against dnaK. Recognizes dnaK from Escherichia coli. This antibody is HRP conjugated. Tested in the following application: ELISA |
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 dnaK Antibody, FITC conjugated |
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| 1-CSB-PA633459HC01EGW | Cusabio |
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Description: A polyclonal antibody against dnaK. Recognizes dnaK from Escherichia coli. This antibody is FITC conjugated. Tested in the following application: ELISA |
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 dnaK Antibody, Biotin conjugated |
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| 1-CSB-PA633459HD01EGW | Cusabio |
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Description: A polyclonal antibody against dnaK. Recognizes dnaK from Escherichia coli. This antibody is Biotin conjugated. Tested in the following application: ELISA |
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 Antibody for Algae DNAK |
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| SPC-301B | Stressmarq | 0.2ml | EUR 366 |
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Description: A polyclonal antibody for DNAK from Algae | Algae (Chlamydomonas reinhardtii). The antibody is produced in rabbit after immunization with Algae Recombinant DNAK of Chlamydomonoas reinhardtii. The Antibody is tested and validated for WB assays with the following recommended dilutions: WB (1:5000). This DNAK antibody is unconjugated. |
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) Polyclonal c-Met Antibody (C-Terminus) |
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| APR02573G | Leading Biology | 0.1ml | EUR 484 |
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Description: A polyclonal antibody raised in Rabbit that recognizes and binds to Human c-Met (C-Terminus). This antibody is tested and proven to work in the following applications: |
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Nitric oxide donor molecules had been additionally merged with kinase inhibitors for most cancers remedy. The present evaluation presents the hybrids designed prior to now 5 years discussing their design rules, outcomes and highlights their future views.
