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.
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 snaphot structures. A synchronous multiple cell view is also available allowing direct comparison of molecules.
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.
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.
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.