The Blue Obelisk—Interoperability in Chemical Informatics

Guha, Rajarshi; Howard, M. T.; Hutchison, Geoffrey; Murray‐Rust, Peter; Rzepa, Henry; Steinbeck, Christoph; Wegner, Jörg K.; Willighagen, Egon

doi:10.1021/ci050400b

Cited by 374 publications

(337 citation statements)

References 20 publications

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“…The crystal structure of versatile peroxidase from P. eryngii (PBD ID: 3FJW) was collected from protein data bank and dispensable chemical components from the raw peroxidase pdb file were deleted manually and missing hydrogen atoms were added using a python script from autodock4 suite (Morris et al 2009). Two-dimensional structures of RB5 and Tween 80 were collected from PubChem database and both these two-dimensional structures were then converted into three-dimensional structures using OpenBabel (Guha et al 2006) software. The processed coordinates were used for docking using SwissDock (Grosdidier et al 2011).…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

Microbial Decolorization of an Azo Dye Reactive Black 5 Using White-Rot Fungus Pleurotus eryngii F032

Hadibarata

Adnan

Yusoff

et al. 2013

Water Air Soil Pollut

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The growth of white-rot fungus Pleurotus eryngii F032 in a suitable medium can degrade an azo dye Reactive Black 5 (RB5), because of its ability to produce ligninolytic enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase that able to degrade and transform the complex structure of the dye into a less toxic compound. The effect of environmental factors such as initial concentration of Reactive Black 5, pH, temperature of growth medium, surfactant (Tween 80), and agitation were also investigated. The productions of ligninolytic enzymes were enhanced by increasing the white-rot fungi growth in optimum conditions. The decolorization of Reactive Black 5 were analyzed by using UV-vis spectrophotometer at the maximum absorbance of 596 nm. The whiterot fungus, P. eryngii F032 culture exhibited 93.56 % decolorization of 10 mg/L RB5 within 72 h of incubation in dark condition with agitation. The optimum pH and temperature for the decolorizing activity was recorded at pH 3 and 40°C, respectively. The addition of surfactant (Tween 80) increased the decolorization to 93.57 % and agitation of growth medium at 120 rpm enhanced the distribution of nutrients to the fungus thus optimized the enzymatic reaction that resulted maximum decolorization of RB5 which was 93.57 %. The molecular docking studies were performed using Chimera visualization software as to analyze the decolorization mechanism of RB5 at molecular level.

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Section: Molecular Docking Studiesmentioning

confidence: 99%

Microbial Decolorization of an Azo Dye Reactive Black 5 Using White-Rot Fungus Pleurotus eryngii F032

Hadibarata

Adnan

Yusoff

et al. 2013

Water Air Soil Pollut

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“…Examples include the Polymath project 40 in mathematics as well as the open generation of cheminformatics tools by the Blue Obelisk group 41 . In such cases the number of participants is smaller than in crowdsourcing projects, but that is because more is being asked of them.…”

Section: Data and Citizen Sciencementioning

confidence: 99%

Open science is a research accelerator

2011

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“…In the simplest form, which is used here, it is initialized by reading the molecular coordinates from an xyz-file. Internally, PyAdf uses the Openbabel library [37][38][39] for storing the molecular coordinates so that any file format supported by Openbabel can be understood. The molecule class of PyAdf has a number of methods for manipulating molecular coordinates (e.g., joining different molecules, splitting a large system into its molecular fragments, adding hydrogen atoms to protein structures, and aligning molecules).…”

Section: Pyadf -Design and Overviewmentioning

confidence: 99%

PyADF — A scripting framework for multiscale quantum chemistry

Jacob

Beyhan²,

Bulo³

et al. 2011

J Comput Chem

101

106

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Abstract:Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PyAdf, a scripting framework for quantum chemistry. PyAdf handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PyAdf and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications.

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The Blue Obelisk—Interoperability in Chemical Informatics

Cited by 374 publications

References 20 publications

Microbial Decolorization of an Azo Dye Reactive Black 5 Using White-Rot Fungus Pleurotus eryngii F032

Microbial Decolorization of an Azo Dye Reactive Black 5 Using White-Rot Fungus Pleurotus eryngii F032

Open science is a research accelerator

PyADF — A scripting framework for multiscale quantum chemistry

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