![]() The search results pages show all CCD and BIRD molecules that match the query parameters.Select InChI or SMILES radio buttons so that the selected descriptor is passed to the Advanced Search as an input along with the selected Match Type parameter.in the documentation for Chemical Search. Learn more about the Match types - "Similar Ligands (Stereospecific)", "Substructure (Stereospecific)", "Exact match", etc. Select the relevant search type from the “Search the PDB” pulldown options.Once the 2D structure of the molecule is drawn or loaded, you can add/remove atoms or groups of atoms using the Marvin JS graphic editor.Īs you edit the molecule, its chemical descriptors (InChI and SMILES) are automatically updated and a "Search" panel appears at the bottom of the page. By clicking on the "Open Chemical Sketch Tool" button in the Chemical Search options in the Advanced Search. The Chemical Sketch Tool can be accessed in two ways:ġ. You can also edit a molecule that is drawn or loaded into the tool to add or remove atoms or groups of atoms and then use the new molecule to query the PDB archive. Both chemical descriptors (SMILES and InChI) of the molecule drawn will be automatically generated and will be available to use as a query. In doing so you can use the graphical interface to draw a molecule of interest or load either the SMILES or InChI descriptors. You can search the PDB archive for a specific ligand or similar ligands based on the 2D chemical drawing of a molecule. The user can then use the descriptor to query the PDB archive for the specific ligand molecule or similar ones. The tool allows users to edit the 2D chemical drawing as needed to automatically generate new chemical descriptors. The Chemical Sketch Tool uses Marvin JS, a web-based chemical sketcher developed by ChemAxon, to quickly and conveniently draw 2D chemical structures from scratch, chemical descriptors (SMILES or InChI), or ligand codes in the wwPDB Chemical Component Dictionary ( CCD). Search for molecular definitions that are substructures of a modified version of CCD ID FMN Introduction What does the Chemical Sketch Tool do? Diversity, Equity, Inclusion, and Access.Citation, Usage, Privacy Policies, Logo.Biologically Interesting Molecule Reference Dictionary (BIRD).The work of Kekule.js has been publish on Journal of Chemical Information and Modeling. Supported Web BrowsersĪll modern web browsers, including ones on mobile devices are supported. ![]() If widget or chem widget modules are used, additional style sheet file also need to be linked in HTML page: Ī tutorial explaining the basic usage of Kekule.js has been made available at here. if Kekule widgets is used, the theme CSS should be imported as wellĪs a JavaScript library, Kekule.js can also be included in HTML page in a traditional way using by tag: Then be imported to your project with ES module import: import from 'kekule' The whole Kekule.js package can be installed with npm: npm install -save kekule Adapter for Indigo lib, support of 2D auto-layout.Adapter for Open Babel, support of many other chemical data formats.Adapter for InChI lib, support of InChI format.2D diagram editor for molecule and other chemical objects.2D or 3D viewer for molecule and other chemical objects.Widgets related to chemistry, including:.Animation system to show/hide those widgets.Small components to be used in web applications, including button, text box, combo box, dialog, tree view, tab view, text editor, color picker, object inspector and so on. ![]()
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