A ‘How To’ on Reproducing Data Obtained During The CHEM6128: Mini Project.

A ‘How To’ on Reproducing Data

Obtained During The CHEM6128: Mini Project

424767301 ‘How To’ Reproduce Results

Contents:

Description: Click on the links to take you to the relative screenshots on ‘How To’. These screenshots will show you how to imitate the steps taken during the mini project.

• ‘How To’ Search for Plasmepsin (PDBe)

• ‘How To’ Convert to Smiles.

• ‘How To’ Convert to InChI.

• ‘How To’ Alternatively Convert to InChI & SMILES.

• ‘How To’ Obtain CAS Numbers.

• ‘How to’ Obtain 3D Structures.

• ‘How To’ Search the CSD.

• ‘How To’ Calculate Descriptors.

• ‘How To’ Calculate Multi-Linear Least Squares QSAR Statistical Model.


‘How To’ Search for Plasmepsin (PDBe):

Firstly you will need to go onto the Protein Data Bank (Europe) and search for Plasmepsin (II).

Next, Click on the tab titled Macromolecules.

Click the arrow to continue:


‘How To’ Search for Plasmepsin (PDBe):

If you then select the title Plasmepsin-2, you will then be taken to a page with all the information on Plasmepsin (II)

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‘How To’ Convert to SMILES:

First the molecule was drawn on ChemBioDraw, then using the convert to structure to name tool the molecular name was obtained


‘How To’ Convert to SMILES.

Then using the Chemspider website (www.chemspider.com), the molecular name was pasted into their search box.Once the molecule is found the SMILES can be found in the relevant identifier section.

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http://www.chemspider.com/


‘How To’ Convert to InChI.

In a similar way to obtaining the SMILES, the InChI is also available in the section below

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‘How To’ Alternatively Convert to InChI & SMILES

If Chemspider doesn’t have the molecule in question, then open Symyx Draw and draw the molecular structure. Then select the chemistry tab and choose from the drop down generate text from structure InChI.

Once chosen you will be provided a text box with either the InChI or SMILES.

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‘How To’ Obtain CAS Numbers.

First open SciFinder, then choose the chemical structure tab in the substances sub heading, then click to edit. Next choose the convert text to structure tool and input the InChI or SMILES obtained previously. Once you obtainthe structure click OK.


‘How To’ Obtain CAS Numbers.

Once you have click OK, Select the search button on the resulting page. Next choose the absolute stereo match tick box. This will then give you the resulting molecule with its CAS number. HOME


‘How to’ Obtain 3D Structures.

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First go onto the resolve option; on chempsider InChIs. Then input the SMILES or InChI of the respective compound, then click search. Once the search is complete, click the 3D tab above the 2D chemical structure.


‘How To’ Search the CSD.

Fist open ConQuest. Choose your searching method. In this case Name/Class was used. The name was then inputted into the compound name section and the add button was selected. After this select your compound name in the contains text box and select the search button. You will then appear on the results tab which will give you a progress bar on the bottom right of the screen.In this case I was unsuccessful in the search. If this happens the

molecule isn’t present in the database. If you search via the draw sections fragments of the molecule can be readily available. This may not seem good, but the fragment approach can be used to estimate log (P).

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‘How To’ Calculate Descriptors.

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First find your molecule in SciFinder, if you’re not aware on how to do this follow the ‘How To’ obtain CAS numbers. Then once you’re on the properties page select the predicted properties and then choose the relevant properties.


‘How To’ Calculate Multi-Linear Least Squares QSAR Statistical Model

First open JMP, then open a new table document. Afterwards input your test/training data into the document, once this is done click the graph option and select graph builder. This will then give you options of dragging and dropping your different axis, allowing for experimentation of trends. If you wanted to change the axis to a reciprocal or a logarithm then right click on the column you would like to do this to then choose transform then your modification.

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A ‘How To’ on Reproducing Data Obtained During The CHEM6128: Mini Project.

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