Plugins

This section is an auto-generated reference for every MolModa plugin, organized by where each lives in the menu. For step-by-step walkthroughs, see the tutorials under Docking and other sections.

MolModa

• About — Get to know MolModa.
• Settings — Modify MolModa general settings.
• Quit — Quit MolModa.

File

Project

• New Project — Start a new project. Your current project will be lost.
• Open Molecule Files — Open (load) molecule file(s).
• Save Molecule Files — Save molecules to the disk.
• Rename Project — Rename the current project.
• Temporary Share — Temporarily share your current session via a link and QR code.

Import

• Load PDB IDs — Load molecule(s) from the Protein Data Bank, a database of proteins, nucleic acids, etc.
• Load AlphaFold Structure — Load a protein from the AlphaFold Protein Structure Database of predicted protein structures.
• Load Molecule from PubChem — Load a compound from the PubChem Database of small molecules.
• Molecular Text — Type or paste molecular text.
• Draw Molecule — Use a molecular editor to draw or edit a small-molecule compound.

Graphics

• Save a VRML2 Model — Save the current molecular scene as a VRML2 file (3D model).
• Save a PNG Image — Save the current view as a PNG file.

Edit

Revisions

• Undo — Undo the last action.

Clipboard

• Copy to Clipboard — Copy the selected molecules to the clipboard.
• Copy SMILES to Clipboard — Copy the selected compound(s) to the clipboard as SMILES strings.
• Paste from Clipboard — Paste a molecule from the clipboard.

Molecules

• Rename Molecule — Rename a molecule.
• Delete Molecule — Delete the selected molecule(s)?
• Merge Molecules — Copy and merge the selected molecules into a single new molecule.
• Clone Molecule — Clone (copy) the selected molecule(s).

Selection

• Select All — Select all molecules in the tree.
• Select Visible — Select all visible molecules.
• Select Invisible — Select all invisible molecules.
• Invert Selection — Invert which molecules are selected in the tree.
• Clear Selection — Clear the selection of all molecules.

View

Toggles

• Toggle Up — Toggle visibility and focus with the molecule above the selected one.
• Toggle Down — Toggle visibility and focus with the molecule below the selected one.
• Toggle Visible — Toggle the visibility of the selected molecules.

Tree

• Expand All — Expand all the nodes in the Navigator panel.
• Collapse All — Collapse all the nodes in the Navigator panel.

Visualizations

• New Visualization — Define a new visualization by specifying selection criteria, representation, and color.

Binding

Analysis

• 2D Interaction Diagram — Use PoseView to generate a 2D interaction diagram showing protein-ligand interactions.

Docking

• Compound Docking/Scoring — Predict the geometry (pose) and strength (affinity) of small-molecule binding.
• Evaluate Docking Performance — Calculate receiver operating characteristic and enrichment factor curves.

Window

• Reset Layout — Resets the panel layout to its default configuration.

Molecules

• Navigator Panel — Switch to the Navigator panel.
• Viewer Panel — Switch to the Viewer panel.
• Styles Panel — Switch to the Styles panel.
• Information Panel — Switch to the Information panel.
• Data Panel — Switch to the Data panel.

Records

• Jobs Panel — Switch to the Jobs panel.
• Log Panel — Switch to the Log panel.

Help

• Documentation — Read the MolModa documentation.
• Plugin Info — List information about each of the loaded plugins.

Example Data

• Append Example Data — Append example data to the current project.

Archived

• Archived Versions — Access previous versions of MolModa.

Compounds

Build

• Protonate/Deprotonate Compounds — Protonate/deprotonate compounds per a given pH, in preparation for docking.
• Rebuild Compound Coordinates — Regenerate small-molecule atomic coordinates.
• Edit Compound — Edit a compound.

Information

• Compound Names — Get the names/synonyms of selected compounds from PubChem.
• PubChem Properties — Get the chemical properties of selected compounds from PubChem.
• PubChem Bioassays — Get the bioassay data of selected compounds from PubChem.

Create Library

• Find Similar Compounds — Build a compound library of chemically similar analogs by searching the PubChem database.

Proteins

• Pocket Detection — Identify small-molecule binding pockets on protein surfaces.
• Align Proteins — Align multiple protein structures to a reference (template) structure.
• Protonate/Deprotonate Proteins — Protonate/deprotonate proteins, in preparation for docking.

Search

• Find Similar Proteins — Find proteins with similar sequences using the RCSB PDB sequence search.

Regions

• Region From Molecule(s) — Create a region that surrounds the specified molecules.
• New Region — Add a new box or spherical region to the project.