Session Import

To use past BMaps sessions, there are two locations from which a saved session may come.

With a downloaded session file, restore by drag and dropping the files into a BMaps window or upload it using the Add Compound button in the upper left.

From a session saved to browser local storage, restore by going to the "GUIDE" button in the upper right of BMaps and press the button under "Load saved session." Please note: browser local storage currently supports only one saved session.

Protein Importing

Proteins may be imported by clicking the protein button in the upper left. Each of the following methods is available as a tab in the menu that will open. Proteins may be imported by clearing the workspace and loading a new structure, or by adding a structure so that the proteins can be aligned and selectivity studies can be performed.

Structure Search

The structure search will search through pre-loaded proteins already loaded by default from BMaps internal servers or from a loaded session file. These files have all been prepared with fragment simulations and water maps so it can save a lot of time to use a pre-loaded protein system if it is relevant to your studies. You can also access the PDB entry for each of the pre-loaded systems via the PDB button the right of each system in the list. A search bar is available to facilitate searching these systems.

Uploading Protein Data

Proteins may also be uploaded via PDB or CIF files by drag and dropping a file, uploading using the upload file search button, or pasting protein data into the import box. The data format must be correctly selected and the upload must be correctly formatted according to the file format standards. A PDB ID and Protein Name can be included to facilitate labeling in the Protein Menu.

Hydrogens may be preserved in the structure using the checkbox.

Name Mapping 

The Name mappings text box allows the user to change the name of an atom, residue, ligand, or chain. This may be needed to achieve compatibility with the Amber forcefield definitions used by energy calculations or other reasons. Multiple name mappings can be included, separated by semi-colons. Note, since a common use case is importing files from Schrodinger's Maestro package, these files are automatically recognized and appropriate name mappings employed, saving you the trouble.

More info can be found on the Name Mappings Page.

Importing From the PDB

Raw PDB files can be imported from the Protein Data Bank website using the 4 letter PDB id. Note that these raw files will not have pre-computed fragment or water maps or hot spots so each of those computations will need to be run for imported structures if needed.

Importing From Alphafold

Proteins can also be imported using a UniProt ID by submitting the sequence to the AlphaFold Protein Structure Database. It is important to note that these structures may have large disordered regions that crystal structure files often leave out because of the low resolution from highly mobile protein components. These will also need any fragment, water, or hot spot analyses to be run on them.

Compound Importing

Compound importing can be accessed through the Add Compound button. You can also drop files or paste data directly into the main workspace at any time to add compounds.

Enter Molecule Data

Molecule data can be entered by Drag and Drop, upload file system menu, or pasting molecular data into the Import Molecule box. This molecular data must be of one of the following file formats: SDF, PDB,SMI,INCHI,CDX,MOL2,CIF,MOL,SD,XYZ,CDXML,CML. You may then give your compound a name that will be used in the Selector Menu Compounds tab.

You can then also decide where you want to place your imported compound to either align with an element of the protein system that is already imported, place outside but near the protein, or keep the existing coordinates of the file. If you currently have a selected atom you can also choose to place the molecule centered on that atom.

By default bond orders are assigned, but this can be toggled off.

2D Sketcher

The 2D sketcher can be accessed in the upper right corner of the Compound Import menu and will open a sketcher using the tool Ketcher. Additional details on how to use this tool can be found in the upper right ? button or in the Ketcher documentation.

CDD Vault

If you are a user of CDD Vault, you can enter the CDD Vault API Key into the provided box and login to your CDD Vault where you can select compounds to import.