MarvinSpace

a high performance 3D molecule visualization tool

3D visualization tool for displaying and manipulating macromolecules. Working with various file formats, users can manipulate in 3D, synchronise views and render high quality 3D visualizations.

Product Type:application
Interfaces:GUI ( Desktop )API ( Java )

Enhanced macromolecular visualization

Wide range of chemical file format support

MarvinSpace opens macromolecule formats such as (list) and several standard chemical structure file formats such as mol, sd or SMILES. Moreover, users can retrieve protein structures connecting to the PDB database and simply typing the PDB code of the protein of interest.

Protein property files, like Gaussian cube files or CHARMM grid files, can also be displayed in MarvinSpace supporting computational chemists and molecular modelers.

File support

High-quality rendering and graphics generation

MarvinSpace records mouse events in a log file therefore viewpoints can be recalled for later analysis. Adjusted rendering can be saved as various standard and custom high quality graphics files, including png, bmp and jpg.

Advanced 3D visualization

All the major surfaces are supported: Connolly, van der Waals, blobby and solvent accessible surfaces can be generated enabling the visual inspection of protein cavities and ligand shape. To ensure performance we have introduced triangle reduction technologies to allow fast interaction even with surfaces for large macromolecules. Surfaces can be coloured by atom and residue type, B-factors, electrostatic potential, or other volumetric data. They are displayed in dotted, mesh, filled, transparent modes. Various customizable property mapping provides flexibility in operation through property mapping, interpolation, superposition and colour blending to generate custom tailored views on docking results or X-ray, NMR or molecular dynamic simulation snapshot structures. A synchronous multiple cell view is also available allowing direct comparison of molecules.

Advanced 3D visualization

Advanced 3D manipulation

Components embedded in a macromolecule file, such as chains, ligands, ions, water, molecules are recognized and classified automatically. Bond angles, distances and dihedrals can be interactively measured and displayed.

File support

Standard 3D visualization

MarvinSpace visualizes macromolecules and chemical structures in wireframe, ball, stick and spacefill and can apply several colouring modes such as cpk, residue, chain or constant. Custom tailored labels are available for atoms, residues and secondary structures. Depth cue, fog effects, clipping panes and anti-aliasing further support high quality graphics generation for publication purposes.

Standard 3D manipulation

All the basic 3D manipulation is offered such as 3D rotation, translation and zoom. Components can be selected, shown, hidden, deleted and faded individually.

Lead optimization support in MarvinSpace

Draw your pharmacophore model

MarvinSpace assigns pharmacophore features to atoms; H-bond donor, H-bond acceptor, hydrophobic, aromatic, anionic, cationic or excluded atom pharmacophore types can be used to build a pharmacophore model.

pharmacophore model

Evaluate your SAR by ligand alignment

Rigid and flexible ligand alignment based on ChemAxon potential function, Maximum Common Substructure and Pharmacophore points can be carried out in MarvinSpace. Therefore overlapping pharmacophore features can easily be investigated.

Moreover, flexible and rigid alignment can also be done within a protein cavity providing preliminary qualitative information on ligand binding facilitating lead optimization processes.

Ligand Alignment

Articles in the library

3D visualization for medicinal chemists

May 28, 2013 - Presentation
A typical medicinal chemist research scenario involves more and more 3D molecular modelling. Current components utilized in visualization and manipulation of experimetal X-ray structures …

Macromolecular Structure Notation, Editing and Registration

Sep 16, 2009 - Presentation
While many software systems exist for small molecule structure representation, drawing and registration and are widely used by biotech/pharmaceutical companies in small molecule drug disc…

Marvin new features and future plans

Sep 15, 2009 - Presentation
Since the last US UGM several new features have been developed in Marvin, and many more are under development. This presentation will summarize these features, and most of them will be de…
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