MIB: Metal Ion-Binding Site Prediction and Docking Server

Lin, Yu Feng; Cheng, Chih Wen; Shih, Chung-Shiuan; Hwang, Jiann Yang; Yu, Chin Sheng; Lu, Chih-Hao

doi:10.1021/acs.jcim.6b00407

Cited by 224 publications

(185 citation statements)

References 19 publications

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“…The side chain conformations and backbone geometry of the designed His were compatible with the CTPR fold and with the metal coordination distances observed in protein coordination sites . The potential of the designed site to coordinate metals was validated computationally using the metal ion‐binding site prediction and docking server . Arrays of three CTPR modules were constructed by combination of H‐modules and WT CTPR units (W‐modules), to obtain CTPR3‐WHW and CTPR3‐HWW proteins, with one H module localized at the central repeat or at the N‐terminal repeat, respectively.…”

Section: Figurementioning

confidence: 95%

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

et al. 2019

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Metal nanoclusters (NCs) are considered ideal nanomaterials for biological applications owing to their strong photoluminescence (PL), excellent photostability, and good biocompatibility. This study presents a simple and versatile strategy to design proteins, via incorporation of a di‐histidine cluster coordination site, for the sustainable synthesis and stabilization of metal NCs with different metal composition. The resulting protein‐stabilized metal NCs (Prot‐NCs) of gold, silver, and copper are highly photoluminescent and photostable, have a long shelf life, and are stable under physiological conditions. The biocompatibility of the clusters was demonstrated in cell cultures in which Prot‐NCs showed efficient cell internalization without affecting cell viability or losing luminescence. Moreover, the approach is translatable to other proteins to obtain Prot‐NCs for various biomedical applications such as cell imaging or labeling.

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Section: Figurementioning

confidence: 95%

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

et al. 2019

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“…A query of the COACH , Profunc , and MIB servers revealed that SIRV1 Rep has the potential to bind several metal ions using His64, His66, and Glu55 (Table ). Notably, Profunc also predicted homology with structures of metal‐free Rep proteins with significant superposition of the metal‐binding residues.…”

Section: Resultsmentioning

confidence: 99%

“…A query of the COACH [12], Profunc [13], and MIB [14] servers revealed that SIRV1 Rep has the potential to bind several metal ions using His64, His66, and Glu55 (Table I).…”

Section: Prediction Of the Sirv1 Rep Metal-binding Sitementioning

confidence: 99%

Design and implementation of structural bioinformatics projects for biological sciences undergraduate students

Oke

Agbalajobi

Osifeso

et al. 2018

Biochem Molecular Bio Educ

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Contemporary biology is currently undergoing a revolution, driven by the availability of high‐throughput technologies and a wide variety of bioinformatics tools. However, bioinformatics education and practice is still in its infancy in most of the African continent. Consequently, concerted efforts have been made in recent years to incorporate bioinformatics modules into biological sciences curriculum of African Universities. Despite this, one aspect of bioinformatics that is yet to be incorporated is structural bioinformatics. In this article, we report on a structural bioinformatics project carried out by final year project students in a Nigerian university. The target protein was the thermoacidophilic Sulfolobus islandicus rod‐shaped virus 1 (SIRV1) Rep protein, which was further characterized using various free, user‐friendly and online sequence‐based and structure‐based bioinformatics tools. This exercise gave students the opportunity to generate new data, interpret the data, and acquire collaborative research skills. In this report, emphasis is placed on analysis of the data generated to further encourage analytical skills. By sharing this experience, it is anticipated that other similar institutions would adopt parallel strategies to expose undergraduate students to structural biology, and increase awareness of freely available bioinformatics tools for tackling pertinent biological questions. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):547–554, 2018.

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“…The interaction of compound 4 with both COX1-1 (2OYU) and COX-2 (3LN1) [11] was carried out using a DockingServer [15].…”

Section: Theoretical Evaluation Of the Interaction Between Compound 4mentioning

confidence: 99%

Synthesis and theoretical activity evaluation of a new steroid-oxazolone derivative against COX1-1 and COX-2

2019

Biointerface Res Appl Chem

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There are some reports for the preparation of several drugs as cyclooxygenase (COX) inhibitors; however, some reagents used in the preparation are expensive and difficult to handle. The aim of this study was to synthesize a steroid-oxazolone derivativeusing some reactions such as i) hydroxylation-amiination; ii) amidation; iii) alkynyl-addition; iv) aldolization and iv) imination. In addition, a theoretical ass was carried out to evaluate the interaction of both COX-1 and COX-2 with the steroid-oxazolone derivativeusing indomethacin and rofecoxib as controls in a docking model. The structure of the compounds obtained was confirmed through elemental analysis, spectroscopy and spectrometry data. The results showed that there are differences between the interaction of the steroidoxazolone derivativewith both COX 1 and COX 2 compared with the bound of indomethacin and rofecoxib with this type of enzymes. These data suggest that the steroid-oxazolone derivativecould be a good candidate as COX-inhibitor translated as a possible drug for treatment of pain.

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MIB: Metal Ion-Binding Site Prediction and Docking Server

Cited by 224 publications

References 19 publications

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

A Simple Approach to Design Proteins for the Sustainable Synthesis of Metal Nanoclusters

Design and implementation of structural bioinformatics projects for biological sciences undergraduate students

Synthesis and theoretical activity evaluation of a new steroid-oxazolone derivative against COX1-1 and COX-2

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