๐ ๐๐จ๐ฅ๐ is live now!๐โฆ.If you have used the RCSB (PDB) structure viewer before (Mol*), you will quickly find ๐๐จ๐ฅ๐ super familiar but more intuitive.
While Mol* offers powerful visualization capabilities, itโs not the most user-friendly tool, especially for basic visualization and rendering operations. This is where ๐๐จ๐ฅ๐ shines, making molecular visualization much more accessible and straightforward.
๐ฅ ๐๐จ๐ฅ๐ is more than just a viewer. It incorporates some user experience from most popular desktop applications that are known for their robust features but limited by their desktop nature, making cloud integration and regular updates challenging. ๐๐จ๐ฅ๐ overcomes these limitations by providing a web-based platform that ensures seamless connectivity to the cloud and facilitates continuous improvements.
๐ฏ ๐๐จ๐ฅ๐ has been designed to integrate major sequence, structure, drugs, and ligands repositories, including the entire PDB (with experimental data), UniProt, and ChEMBL and more.
Key Features of ๐๐จ๐ฅ๐:
1๏ธโฃ ๐๐ป๐ต๐ฎ๐ป๐ฐ๐ฒ๐ฑ ๐จ๐๐ฎ๐ฏ๐ถ๐น๐ถ๐๐: ๐๐จ๐ฅ๐โs intuitive interface makes it easier than ever to visualize complex biomolecular structures.
2๏ธโฃ ๐๐ถ๐ด๐ต-๐ฃ๐ฒ๐ฟ๐ณ๐ผ๐ฟ๐บ๐ฎ๐ป๐ฐ๐ฒ ๐ฉ๐ถ๐๐๐ฎ๐น๐ถ๐๐ฎ๐๐ถ๐ผ๐ป: ๐๐จ๐ฅ๐ supports the simultaneous visualization of hundreds of protein structures, molecular dynamics trajectories, and cell-level models at atomic detail. Handle models with tens of millions of atoms with impressive efficiency.
3๏ธโฃ ๐ฆ๐ฒ๐ฎ๐บ๐น๐ฒ๐๐ ๐๐ฎ๐๐ฎ ๐๐ป๐๐ฒ๐ด๐ฟ๐ฎ๐๐ถ๐ผ๐ป: Connect ๐๐จ๐ฅ๐ to a plethora of databases and data management tools within the Genophore platform or with your own. Effortlessly access and manage your data, enhancing your workflow and productivity.
4๏ธโฃ ๐๐ผ๐บ๐ฝ๐๐๐ฎ๐๐ถ๐ผ๐ป๐ฎ๐น๐น๐ ๐๐บ๐ฝ๐ผ๐๐ฒ๐ฟ๐ฒ๐ฑ: Experience the power of modern AI and ML algorithms integrated into ๐๐จ๐ฅ๐. From predictive modeling to generative design, ๐๐จ๐ฅ๐ provides a comprehensive solution for your molecular visualization needs (coming soon, contact us for early access!).
Intuitive Interface Design
The MolX interface is designed to be intuitive and easy to navigate, ensuring that users can quickly access the tools they need for molecular visualization. Here are some key elements of the interface:
- Sequence Viewer: At the top of the interface, users can view the amino acid sequence of the protein, providing a quick reference for sequence-based analyses.
- Toolbar: A set of icons in the toolbar above the 3D structure display area offers various visualization options, allowing users to switch between different display modes and color schemes with a single click.
- 3D Structure Viewer: The main area is dedicated to the 3D visualization of the molecular structure, where users can interact with and explore the model in detail.
Advanced Visualization Options
MolX provides a range of advanced visualization options to suit different analytical needs:
- Color by N to C Terminus: This option colors the protein based on the position from the N-terminus to the C-terminus using a gradient color scheme. This helps in understanding the sequence progression and identifying terminal regions.
- Color by Chain: This view highlights different chains within the protein structure using distinct colors. It makes it easy to differentiate between multiple chains in complex proteins or protein assemblies.
- Color by B Factor: Visualizing the structure based on B factor values, which indicate atomic displacement or flexibility, allows researchers to identify regions of the protein that are more dynamic.
- Color by Accessible Surface Area: This mode colors the structure according to the accessible surface area, which is crucial for identifying exposed regions that may be important for interactions with other molecules.
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Display Modes for Detailed Analysis
MolX offers several display modes that cater to different visualization preferences and requirements:
- Display Balls: In the ball-and-stick model, atoms are represented as spheres, providing a detailed view of atomic interactions and bond geometry.
- Display Sticks: The stick representation emphasizes the connectivity and bond angles between atoms, making it easier to study the molecular framework.
- Display Surface: Rendering the molecular surface gives a clear sense of the protein's shape and surface topology, essential for understanding surface interactions and binding sites.
Nucleic Acids Visualization
- Cartoon Representation: Highlights the helical structure of DNA and the folds and loops of RNA with color-coded chains.
- Stick Representation: Shows detailed atom and bond interactions for examining specific interactions like hydrogen bonds.
- Surface Representation: Generates molecular surfaces to visualize shape, accessibility, and interaction surfaces.
- Base Pairing and Stacking: Highlights base pairing (e.g., A-T, G-C) and stacking interactions with tools for visualizing hydrogen bonds and measuring distances.
- Annotations and Labels: Allows adding labels and annotations to specific nucleotides or regions.
Ligand Interactions
MolX provides robust capabilities for visualizing and analyzing ligand interactions with biomolecules. Key features include:
- Ligand Binding Site Identification: Automatically detects and highlights ligand binding sites, allowing users to easily locate and examine these regions.
- Visualization Modes: Supports various visualization modes for ligands, including stick, ball-and-stick, and surface representations, helping users understand the spatial relationships and interactions between ligands and biomolecules.
- Interaction Analysis: Tools to visualize and analyze interactions between ligands and their binding sites, such as hydrogen bonds, hydrophobic contacts, and electrostatic interactions. Users can easily identify key residues involved in binding.
- Distance Measurements: Enables precise distance measurements between ligand atoms and protein residues, facilitating detailed interaction studies.
- Surface Representation: Displays the molecular surface of the ligand and its binding site, highlighting pockets and grooves that accommodate the ligand.
- Binding Affinity Predictions: Integrates with computational tools to predict binding affinities and visualize the strength and stability of ligand interactions.
- Dynamic Visualization: Supports the visualization of ligand interactions over time using molecular dynamics simulation data, showing how ligands interact with their targets dynamically.
Stay tuned for more updates and demonstrations of ๐๐จ๐ฅ๐โs capabilities.