ChemSpider: An Online Chemical Information Resource

Pence, Harry E.; Williams, Antony J.

doi:10.1021/ed100697w

Cited by 984 publications

(641 citation statements)

References 6 publications

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“…FGs contained in α-pinene and 1,3,5-trimethylbenzene photooxidation products defined in MCMv3.2 (Jenkin et al, 1997;Saunders et al, 2003;Jenkin et al, 2003;Bloss et al, 2005), obtained via http://mcm.leeds.ac.uk/ MCM; 2. FGs that are measured or measurable (i.e., have absorption bands) for FTIR analysis (Pavia et al, 2008); 3. molecular fragments used by SIMPOL.1 for estimation of pure organic compound vapor pressures;…”

Section: Introductionmentioning

confidence: 99%

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Ruggeri

Takahama

2016

Atmos. Chem. Phys.

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Abstract. Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apportionment, and various models based on a group contribution framework have been developed to calculate physicochemical properties of organic compounds. In this work, we provide a set of validated chemoinformatic patterns that correspond to (1) a complete set of functional groups that can entirely describe the molecules comprised in the α-pinene and 1,3,5-trimethylbenzene MCMv3.2 oxidation schemes, (2) FGs that are measurable by Fourier transform infrared spectroscopy (FTIR), (3) groups incorporated in the SIMPOL.1 vapor pressure estimation model, and (4) bonds necessary for the calculation of carbon oxidation state. We also provide example applications for this set of patterns. We compare available aerosol composition reported by chemical speciation measurements and FTIR for different emission sources, and calculate the FG contribution to the O : C ratio of simulated gasphase composition generated from α-pinene photooxidation (using the MCMv3.2 oxidation scheme).

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Section: Introductionmentioning

confidence: 99%

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Ruggeri

Takahama

2016

Atmos. Chem. Phys.

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“…The structures of four CypA inhibitors, Alisporivir, NIM811, SCY635, and Sanglifehrin A were obtained in SDF format from ChemSpider database [23]. As shown in Table 1, the sequences and validated structures of CypA, Annexin II, and Rab7 as well as relative HBV receptors were obtained from protein databank (PDB) [1].…”

Section: Methodsmentioning

confidence: 99%

Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors

Mohebbi¹,

Mohammadi

Memarian

2016

VirusDis.

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Hepatitis B virus (HBV) is an etiological agent of viral hepatitis, which may lead to cirrhosis, and hepatocellular carcinoma. Current treatment strategies have not shown promising effect to date but various complications such as, drug toxicity-resistance have been reported. Study on newly discovered compounds, with minimal side effects, as specific HBV inhibitors is a fundamental subject introducing new biologic drugs. Here, we aimed to, by prediction, estimate interactions of HBF-0259 as a nontoxic anti-HBV compound on inhibiting the HBV through either interaction with the viral entry or HBsAg secreting factors using In Silico procedure. Molecular docking was performed by Hex 8.0.0 software to predict the interaction energy (Etot) between HBF-0259 and known cellular factors involved in HBV entry and HBsAg secreting factors. Hex 8.0.0 also employed to create protein-protein complexes. These interactions were then used to analyze the binding site of HBF-0259 within the assumed receptors by MGLTools software. Finally, the amino acid sequences involved in this interaction were aligned for any conservancy. Here, we showed that HBF-0259 Etot with CypA (-545.41 kcal/mol) and SCCA1 (499.68 kcal/mol), involved in HBsAg secretion and HBV integration, respectively, was higher than other interactions. Furthermore, HBF-0259 predicted interaction energy was even higher than those of CypA inhibitors. In addition, we claim that preS1 and/or preS2 regions within HBsAg are not suitable targets for HBF-0259. HBF-0259 has higher interaction energy with CypA and SCCA1, even more than other known receptors, co-receptors, viral ligands, and secretory factors. HBF-0259 could be introduced as potent anti-viral compound in which CypA and or SCCA1, as previously shown, are involved.

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“…[12] A reliable chemical representation makes it possible to generate standard InChIs [13] that can be used to establish interoperability between the CSD and other chemical and biological resources. Links have thus far been established between ChemSpider, [14] PubChem, [15] and the Protein Data Bank. [16] The CSD is part of a wider ecosystem comprising the technical and social components needed to make crystal structure data available in support of published research and for reuse in the pursuit of new discoveries.…”

Section: Reproducibility Validation and Reuse Of Crystal Structure Datamentioning

confidence: 99%

From Experiments to Knowledge

Bruno¹

2017

Chemistry International

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ChemSpider: An Online Chemical Information Resource

Cited by 984 publications

References 6 publications

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Prediction of HBF-0259 interactions with hepatitis B Virus receptors and surface antigen secretory factors

From Experiments to Knowledge

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