3D Protein visualisation tool manual

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Overview

The protein structure visualization tool is an AI-powered module integrated into the LensAI™ portal. It enables users to analyze and visualize protein structures using natural language commands through a chatbox interface. The tool is designed to support scientific exploration of molecular data without requiring technical knowledge or programming expertise.

This functionality is particularly useful for users working with structural biology, protein modeling, and interaction analysis. By leveraging large language models (LLMs), the tool translates plain English input into complex visualization and selection commands, facilitating easy, interactive and targeted structural analysis.

Accessing the tool

To use the Smart Visualization Tool:

Navigate to your dataset and open any PDB file.
Click on the "View" icon

Figure 1: Navigating to a dataset and selecting a PDB file (e.g., 6W2C.pdb)
Once opened, a 3D structure viewer is launched. On the left, you will see the chat box, at the right the protein itself is visualized.
LLM Question – for natural language interaction

Figure 2: Smart visualization interface within the BioStrand Portal, with input boxes and 3D model viewer
Click the question mark (?) beside either input box to view example commands.
Type your question or command in plain English (e.g., “Show ASP98 and highlight residues within 5 Å”) and click Run.

Capabilities

Functionality	Description
Natural Language Input	Accepts plain English commands to manipulate molecular models.
3D Protein Visualization	Provides interactive 3D representations (rotate, zoom, pan).
Residue and Atom Selection	Allows precise selection based on residue type, atom name, proximity, or structural features.
Color Mapping	Enables visual distinction using color coding based on residue properties (e.g., hydrophobicity, secondary structure).
Labeling	Supports the addition of labels to selected elements for annotation.
Distance-Based Queries	Identifies atoms or residues within a defined distance of a specified reference point.
Secondary Structure Analysis	Highlights α-helices, β-sheets, or loops based on structural context.
Ligand Interaction Assessment	Enables analysis of residue-ligand proximity

Basic usage

Once you have successfully opened a PDB file within the protein structure visualization tool, you can start interacting with the molecular model by entering commands into the designated input field. This intuitive interface allows you to communicate with the tool using natural language or syntax-based queries, depending on your preference and expertise. As you type your commands, the tool's advanced AI algorithms will interpret your input, translating it into precise actions that are applied directly to the molecular model. This process enables you to manipulate the 3D structure in various ways, such as highlighting specific residues, coloring regions based on their properties, or selecting atoms within a certain distance. By leveraging this functionality, you can conduct detailed analyses and gain insights into the molecular structure without needing extensive technical knowledge or programming skills.

Common commands

Show ASP 98
Highlight chain A
Color residues by hydrophobicity
Show all residues within 5 Angstrom of RFY 705
Add labels
Choose atoms named "C", "O", "N", or "CA"
Color blue the polymer within 2.5 of solvent

Smart Visualisation Tool - Figure 3

Figure 3: Example output showing hydrophobic coloring and residue selection

Example scenario

Use case: Structural analysis of Asp98 in SERT (PDB: 6W2C)

This example illustrates a step-by-step analysis of Asp98 within the serotonin transporter to assess its interaction with the ligand I-paroxetine (RFY).

Steps

I would like to show ASP 98
Show all residues within 5 Angstrom of ASP 98 in chain A
Select 705 in purple and add a label
Color residues by hydrophobicity
Color blue the helices residues

Objective

These commands collectively help determine the proximity of Asp98 to the ligand, the local hydrophobic/hydrophilic environment, and whether Asp98 is part of a stable secondary structure. This information can be used to hypothesize its potential role in ligand stabilization or protein structural integrity.

Figure 4: Screen recording of this use-case commands execution.

Supported command patterns

Selection commands

Command	Description
`Select hydrophobic_residues`	Selects all hydrophobic residues.
`Choose all alanine residues`	Selects all alanines (ALA).
`Choose atoms named "C", "O", "N", or "CA"`	Selects common backbone atoms.
`Choose all alanine residues in 5 Angstrom distance from the residue 5`	Spatial residue selection.
`Choose all residues with helix secondary structure`	Selects all helix-forming residues.
`Choose all residues with sheet secondary structure`	Selects all residues forming β-sheets.

Visualization commands

Command	Description
`Color residues by hydrophobicity`	Applies a color scale based on residue hydrophobicity.
`Color red the residues within 5 Angstrom of RFY`	Highlights spatial neighbors of the ligand.
`Color blue the polymer within 2.5 of solvent`	Highlights protein regions close to solvent molecules.
`Add labels`	Adds residue or atom labels to the selection.

Best practices

Use clear, unambiguous language.
Specify chain identifiers when necessary (e.g., “Asp98 in chain A”).
Combine selection, coloring, and labeling for detailed visualizations.