Step-by-Step Explanation:

On the Advanced Search page, you can simultaneously select multiple filtering parameters:

1. Text Search: A Text Search field allows you to filter using the name of the molecule (INN or drug code). The search box has a matching dropdown menu that can help you find the molecule of interest. Long dropdown menus can be explored by scrolling down the dropdown menu pop-up.
2. Free Text Search: A Free Text Search field allows you to search for specific text in any column of the dataset.
3. Molecular characteristic variables:
   • General molecular category: Examples include ADC, bispecific, multispecific, and immunoconjugate.
   • Target antigen: To filter by target antigen, there is a Text Search field with a matching dropdown menu. As an antigen can be known by different names, you can use the synonym list to find the correct antigen name to use in the search.
   • Format: General format categories such as full-length, fragment, or appended Ig.
   • Heavy and light chain isotype
   • Variable region sequence source
4. Clinical development variables:
   • Status:
     • General status (e.g., preclinical, clinical, approved)
     • More specific status, such as the most advanced stage of development (e.g., Phase 1, Phase 2, Phase 3)
   • Date of milestone clinical development event: You can also filter the data by the date of a milestone clinical development event. The type of milestone clinical development event can be selected using a dropdown menu, and the time range can be selected using a slide bar. This allows you to limit searches to yield results for development in specific periods.
   • Primary therapeutic area of development
   • Location of the company developing the molecule

To reset the filtering criteria to default, click on the grey Reset filters button. The default selected options allow display of the complete dataset. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to filter by name of the molecule

On the Advanced Search page, a Text Search field named “Molecule name (INN, drug code)” allows you to filter using the name of the molecule, either the INN (when applicable) or the drug code.

As shown in the example below, when you start typing in the search box, a matching dropdown menu pops up to help you find the molecule of interest. Long dropdown menus can be explored by scrolling down.

What is this feature useful for?

• Searching for a specific molecule. Example: you can type a specific drug code, or INN.
• Exploring the database using the antibody portion (or the drug portion, when applicable) of an INN. Examples: if you type “trastuzumab”, the results will include all antibodies with “trastuzumab” in their INN; if you type “deruxtecan”, the results will include all antibodies with “deruxtecan” in their INN.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

What to expect from the Free Text Search

A Free Text Search field allows you to search for specific text in any column of the dataset and is located near the bottom of the Advanced Search page.

As the feature will return entries containing the text in any column of the dataset, you need to carefully choose what to type in the search field.

What is this feature useful for?

[Tags (work in progress) ]
You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to use the General Molecular Category filter

The general molecular category filter allows you to limit results to a certain molecular category or combination of molecular categories.
This tutorial will explain the rationale behind our general molecular category classification and provide a step-by-step guide on how to use the general molecular category filter on the Advanced Search panel.
Therapeutic antibodies now include complex molecules that might belong to different or multiple molecular categories.
To develop the YAbS database, we classified therapeutic antibodies according to the following features: specificity, conjugation status, composition (i.e., one molecule or a mixture of two or more), mechanism of action, and antigen binding properties, as represented in the schematic below.

We used one or more of these categories to annotate the general molecular category of our molecules:

1. Specificity: A therapeutic antibody can be monospecific, bispecific, or multispecific. If bispecific or multispecific, the molecule can bind to different antigens or different epitopes on the same antigen. When designed to bind different epitopes on the same antigen, we annotated the general molecular category of the molecule as “Biparatopic” or “Multiparatopic”.
2. Conjugation status: Antibodies can be naked, chemically conjugated to other molecules, or genetically fused to non-Ig proteins or protein domains. With the exception of ADCs and Radioimmunoconjugates (RIC), we classify everything that is conjugated to other molecules (e.g., PEGylated, biopolymer conjugated, immunoliposomes, antibodies for photoimmunotherapy, unconventional ADCs) or fused to non-Ig proteins or protein domains (e.g., immunotoxins, immunocytokines, bispecific/multispecific immunoconjugates) as Immunoconjugates. Molecules annotated as Immunoconjugates and Unconventional ADCs are also annotated with specific categories (e.g., Antibody Degrader Conjugate, Immune-Stimulating Antibody Conjugate (ISAC), Antibody Oligomer Conjugate (AOC), Antibiotic Conjugate, Steroid Conjugate).
3. Composition: Antibody therapeutics can also be formulated as one molecule or a mixture of molecules. When formulated as an antibody mixture, we annotated the general molecular category of the molecule as “Mixture,” and, when known, we specify the number of molecules in the mixture.
4. Mechanism of action: Antibody therapeutics can have a canonical mechanism of action (blocking, agonist, antigen clearance, cell-mediated effector function, payload delivery) or be designed as vaccines. When designed as a vaccine, we annotated the general molecular category of the molecule as “Vaccine.”
5. Antigen binding properties: Antibody therapeutics can be designed with canonical antigen binding properties or be conditionally active. When designed as conditionally active, we annotated the general molecular category of the molecule as “Conditionally active.”

Here we provide a step-by-step guide on how to use the General Molecular Category filter on the Advanced Search panel.

If the General Molecular Category filter is not used and you click the Submit button, the results will include all general molecular categories.
The General Molecular Category filter allows you to restrict the search to a specific general molecular category or a specific combination of general molecular categories.
The General Molecular Category dropdown menu shows all possible general molecular categories.

If you select one category, the results will show all entries that have the name of the selected category in the “General Molecular Category” column.
If you select more than one category, the results will include only entries that have all names of the selected categories in the “General Molecular Category” column. Entries whose General Molecular Category includes only one (or more than one but not all) of the selected categories will not be included in the results. This is because the feature uses the function AND, not the function OR.
If multiple categories are selected and the Results page shows no entries, it means that there are no entries which are labelled with all the selected molecular categories.

What is this feature useful for?

• This filter allows you to restrict the search to a specific general molecular category or a specific combination of general molecular categories.
• Examples:
  • By selecting a broad category, such as “ADC,” the results will include all entries that have the name of the selected category in the “General Molecular Category” column, including ADC, ADC that are also bispecific, and molecules that are unconventional ADC. Another example of a broad category is “Mixture.” If this category is selected, the results will show all molecules formulated as a mixture, regardless of the number of molecules in the mixture.
  • As an example of a narrower search, you can select “Unconventional ADC.” This result will show all unconventional ADCs, but not canonical ADCs.
  • As one molecule can be represented by multiple general molecular categories, the filter can be used to restrict the search to a specific combination of molecular categories. One example is bispecific ADCs. To restrict the search to molecules that are both ADC and bispecific, you need to select both “ADC” and “Bispecific” categories. The results will include only molecules that are both ADC and bispecific and will not include molecules that are only ADC or only bispecific.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to use the format, general category filter

The format, general category, filter allows you to limit results to a certain format category.
This tutorial will explain the rationale behind our general format category classification and provide a step-by-step guide on how to use the format, general category, filter on the Advanced Search panel.
To develop the YAbS database, we standardized the nomenclature we use to annotate antibody therapeutics. The format category encompasses full-length antibodies, antibody fragments with or without an Fc, and appended Igs. Fragments may contain one or more Ig domains that bind antigens (e.g., VH, VL, VHH, Nanobody), scFv, dsFv, Diabody, DART, Fab, F(ab)2). Fragment-Fc are composed of one or multiple antibody fragments fused to an Fc, while appended Ig are full-length Ig fused to one or multiple antibody fragments. Each of these formats can be naked, conjugated to other molecules such as small-molecule drugs or fused to non-Ig proteins. We annotated the general format of our molecules according to the following schematic.

We also annotated format details according to the following schematic, but, since limited information is available for molecules in preclinical or early-stage clinical development, we chose not to add a search parameter based on this variable to the Advanced Search panel. When available, you can find the information regarding format details by looking at the Format details column in the table on the Result page.

To use the format, general category, filter on the Advanced Search panel, select one or multiple options from the dropdown menu.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to filter by target antigen(s)

The Target antigen(s) filter located on the Advanced Search panel allows you to limit results to molecules targeting a certain antigen or combination of antigens.
The Target antigen(s) filter consists in a Text Search field with matching dropdown menu.

To use the filter, type the name of the antigen of interest in the Text Search box and a dropdown menu will appear.
An antigen can be known by different names, but only one name will be recognized by our filter function.
Example: if you type CD137 in the Target antigen(s) search field, no dropdown menu will appear. This is because CD137 is not the name we chose for the filter feature.

We therefore created a list of synonyms for each antigen. You can check our synonym list to find the antigen name to use in the search by clicking on “Click here to view the target list”.
On the synonym list page, you can scroll down to see all antigens featured in the database. To find the correct name to use with the search by target filter, you can type the target name in the text search filter.

When text is typed in the search box, the synonym list is filtered, showing all rows containing the typed text. The antigen name to use for the Target antigen(s) filter is shown in the column named "Target", all synonyms are shown in the column named "Synonyms".
Example: if you type "CD137", the filtered list shows that the antigen name to use for the Target antigen(s) filter is "4-1BB".

You can go back to the Advanced Search panel using the browser "Back" button, and use the correct name on the Target antigen(s) filter.
Example: if you type "4-1BB", a dropdown menu appears, and you can select 4-1BB only or 4-1BB in combination with other targets. If you select 4-1BB only, the Results will show all antibodies targeting 4-1BB, including monospecific antibodies targeting 4-1BB only, and bispecific/multispecific antibodies simultaneously targeting 4-1BB and other targets.

What is this feature useful for?

1. This filter allows you to restrict the search to antibodies targeting a specific antigen or combination of antigens, as shown in the examples above.
2. The synonym list allows you to browse all antigens targeted by the antibodies in the database and select the correct antigen name to use in the search by target text box, as shown in the examples above.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to filter by clinical development status

Each molecule in the database is annotated with two types of clinical development status:

1. General status: (e.g., approved, terminated, clinical, preclinical, withdrawn, IND, emergency use, no development reported)
2. More specific status: Such as the most advanced stage of development (approved in which country, most advanced phase when it was terminated, most advanced phase currently in the clinic).

The filter by clinical development status is located in a light blue box on the Clinical development section of the Advanced Search panel.

You can use toggles to select if you want to filter by general or more specific status. A dropdown menu allows you to choose one or more specific status.
When selecting the General development status category toggle, the dropdown menu will allow you to choose one or more of the following options: approved, terminated, clinical, preclinical, withdrawn, IND, emergency use, no development reported.

When selecting the Most advanced stage of development (global) toggle, the dropdown menu will allow you to choose a more specific status for approved, clinical and terminated molecules as in the three examples below:

1. Approved
   
   
2. Clinical
   
   
3. Terminated
   
   

You can deselect the options not of interest by deselecting the appropriate tick boxes in the first dropdown menu. To quickly select the options of interest, click on the tick boxes on the first menu to deselect the ones not of interest, and, when applicable, click on the ones of interest in the second dropdown menu.
You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

Limit searches to yield results for development in specific periods: a step-by-step guide

This is a step-by-step tutorial on how to limit searches to yield results for development is specific periods using the filter by date function. The filter by date function allows you to filter the data by date of a milestone clinical development event.

Steps to Use the Date Filter

1. On the Database homepage, click on the “Advanced search” button.
   
2. On the Advanced Search panel, use the “Choose column and search by date” feature located in the “Clinical development” section on the right-hand side.
   
3. The type of milestone clinical development event can be selected using a dropdown menu, and the time range can be selected by moving the toggles on the slide bar.
   
   
4. Once you have selected the type of milestone clinical development event and the desired time range, click on the “Submit” button. You can also combine this search with other desired parameters.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to filter by primary therapeutic area of development

The Primary therapeutic area filter located on the Advanced Search panel allows you to limit results to molecules developed for one or more specific therapeutic areas.

To filter by primary therapeutic area, select one or multiple options from the dropdown menu.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to filter by location of the company developing the molecule

The Location of the company filter is located on the Advanced Search panel and allows you to limit results to molecules developed in specific countries or regions.

To filter by region or country of the company developing the molecule, select one or multiple options from the dropdown menu. A first dropdown menu allows you to choose the specific region.

For each region, a second dropdown menu allows you to choose the specific country. The example below shows the choice of countries for the Asia region.

You can use this search parameter alongside other parameters on the Advanced Search panel. Once you have selected your filtering options, click the blue Submit button, and you will be taken to a Result page, where you can further refine your query and export the results.

How to refine your Advanced Search panel on the Result page

This is a step-by-step tutorial on how to refine your search when on the Results page.

1. After selecting the desired parameters and clicking the Search button on the Advanced Search panel, a Results page will be displayed. This Results page is divided into two sections. The section at the top has pie charts and associated filtering boxes to further refine your search. The bottom section has a table showing detailed data for the filtered antibody entries, which can be browsed and exported.
   
   
2. The pie charts give a graphical overview of the filtered results in terms of general development status, general molecular category, therapeutic area, and target. To see the legend of each slice, hover over the pie chart slices. On top of each pie chart, there is a filtering text search box that allows further filtering. To refine your search, you can type in one or more Text Search boxes and click on the blue “Filter” button. To reset these filters, delete the text in the search boxes and click on the “Filter” button again, this will reset the search box filters, but the eventual filters used on the advanced panel will stay.
   
   
3. Once you click the “Filter” button, the Result page will reload and show the filtered results in the form of pie charts and a table. Results can be browsed, and the table can be exported in .csv format.
   In the example below, the results have been refined using all the four Text Search boxes.