ICM-Browser-Pro

ICM-Browser-Pro is an advanced molecular visualization and analysis software developed by Molsoft L.L.C., designed for researchers and scientists working with 3D protein structures, crystallographic data, and molecular sequences. It is available on Windows, Mac, and Linux platforms, and extends the capabilities of the free ICM-Browser with a comprehensive suite of structural analysis, movie-making, and crystallographic tools.

ICM-Browser-Pro builds upon all the features found in ICM-Browser — including ligand binding pocket surface display, PDB search, hydrogen optimization, surface rendering, protein structure superimposition, and measurement of angles and distances — while adding powerful additional capabilities suited for more in-depth structural research workflows.

Molecular Visualization and Movie Making

• Create molecular movies by capturing on-screen displays and exporting to *.mpeg, *.avi, or *.mov file formats.
• Pause and modify scenes during movie creation, and include smooth transitions between positions.
• Display high-quality shadow representations and save images with these shadow effects.
• Connect selected molecules to the mouse for independent rotation and translation relative to the original coordinate frame.

Structure Analysis Tools

• Calculate protein contact areas, closed cavities, and surface area.
• Display distances and angles interactively within the 3D viewer.
• Generate and interact with fully interactive Ramachandran plots.
• Superimpose multiple protein structures using specific interatomic pairs, 3D alignment, aligned residues, residue number, or exact match, with user-defined atom selections.
• Automated protein secondary structure assignment using an ICM modification of the DSSP algorithm (Kabsch and Sander, 1983), based on observed hydrogen bond patterns in 3D structures.

Crystallographic Analysis Tools

• Direct link to the electron density map repository for streamlined access to crystallographic data.
• Contour electron density maps for entire molecules.
• Generate crystallographic cells, neighbors, and biomolecular assemblies.

Surface and Electrostatics Display

• Display molecular surfaces colored by binding properties and electrostatics.
• Edit surfaces and meshes, and export them as Wavefront object files for use in external applications.

Sequence and Alignment Tools

• Read and display biological sequences and alignments.
• Extract sequences directly from 3D structures.
• Apply multiple coloring schemes to sequence alignments.
• Annotate sequences and alignments with connection to the corresponding 3D structure.

Plotting and Data Visualization

• Generate fully interactive, colorful X-Y plots and histograms.
• Support for up to 4-dimensional data representation within plots.

ICM-Browser-Pro can be extended further through ICM-Pro, a superset platform from Molsoft that incorporates all ICM-Browser-Pro features alongside additional tools for structure prediction, molecular docking, mutation modeling, electrostatic and energy calculations, structure annotation, ligand pocket and protein interface analysis, compound property assessment, alignment building and editing, and mathematical modeling.