Tips & Tricks

To communicate with EMLy, type a message in the chat box and EMLy will respond as appropriate. There are a number of different tools you can use to analyse a molecule, but first you will need to choose which molecule to analyse. This can be done by giving EMLy your chosen protein sequence by uploading a file by pressing the paperclip icon in the bottom left corner of the chat box, or typing the sequences into the chat box. There are also databases EMLy can access from which you can ask for a specific molecule which will be returned as a Protein Data Bank (PDB) file. These databases include RCSB Protein Data Bank, SAbDab, GenBank, AlphaFoldDB, and Etcembly’s own database. 

To the right of the Recent Chats tab at the top of the screen, there are 4 different tabs for data analysis/viewing within EMLy. These are 3D Viewer, Data, Graphs, and Example Sequences. The 3D Viewer tab will show the structure of the molecule with different regions highlighted, as well as visualise results from various processes like renumbering or electrostatic patches analysis. Some functions will return csv or fasta files of data that are ready to be downloaded but these files can also be seen in the Data tab. For example, when annotating a molecule, the full numbering tables for light and heavy chains are displayed here. When performing sequence alignment, a table is displayed here that highlights the sequences’ similarities and differences relevant to antibody engineering.

For most questions asked, above the output there is a dropdown menu entitled ‘Reasoning and Tools’. This menu will say the tool used to get the output given, and the output received by that tool. In some more complex work flows, more than one tool is used. In these circumstances, the tool used and then the output given are listed one after the other. If you ask a question that does not use any tools like how does this concept work or why has this happened, no tools are used so no reasoning and tools drop down menu appears.

To delete a chat, go to the Recent Chats tab, click on the chat you want to delete and then the rubbish bin icon next to the + icon.

After displaying a molecule in the 3D Viewer tab, this molecule can be analysed in various ways, for example renumbering or humanising it. Ask EMLy to perform the operation needed (eg: ‘renumber this molecule’, ‘humanise this molecule’). It is also possible to ask EMLy for help when using it, it can help you if you are not sure how to use it to do something. It can also provide a list of its tools if needed with the prompt ‘list all tools’.

Some of the functions EMLy can help with include renumbering, humanising, or annotating the molecule. To do your desired function, ask EMLy to perform that tool, for example by typing ‘renumber this molecule’ or ‘humanise this molecule’. Sometimes EMLy will need additional parameters for functions like codon optimisation. It will ask you to provide these when needed, as well as giving example options which can be used. The tools section of this knowledge base contains a complete list of all tools currently available within EMLy, as well as a brief guide to their expected inputs and outputs, as well as a description of how they work and why they are important. These tools are organised into different folders - biobetter, codon optimisation, antibody expression, and general in accordance to the agents they belong to.