Molecule World5.0

A modern 3D molecular workspace that makes exploring the connections between sequence, structure, and function accessible to a new generation of scientists, educators, and students.

Molecule World 5.0 is built for how molecular structures are explored and designed today. View, compare, align, and explore experimental structures and computationally generated models together. Compare normal and mutant proteins, investigate structural differences, and connect sequence changes to their 3D consequences.

Explore proteins, DNA, RNA, and small molecules on iPhone, iPad, and Mac. Rotate, zoom, and pan through structures with high-quality interactive 3D visualization. Molecule World brings structure viewing, sequence analysis, molecular comparison, and educational tools together in one app.

EXPERIMENTAL AND COMPUTATIONAL STRUCTURES

Open structures from X-ray crystallography, cryo-EM, and NMR alongside computationally generated models. Search RCSB PDB, NCBI MMDB, and PubChem by ID or keyword and download structures directly into your library.

SEQUENCE AND STRUCTURE

The sequence viewer on iPad and Mac shows every chain as a row of residues colored to match the 3D view. Copies of a molecule line up in shared columns, while superimposed models read down the same columns. See sequence differences in context and investigate their structural consequences.

POWERFUL VISUALIZATION

Choose Spacefill, Ball & Stick, Tubes, Ribbon, Surface, or Wire Surface representations. Color by element, secondary structure, chain, sequence, assembly, conserved domain, residue type, charge, hydrophobicity, or B-factor. Show proteins, nucleic acids, or chemical components alone, or reduce chains to their backbone or Cα trace. A color key shows what is on screen, while the Info card reports what a structure is, how it was determined, and what it contains.

YOUR LIBRARY

Keep structures in folders, synced through iCloud Drive or stored on the device. Filter your library by atoms, chains, resolution, confidence values, file type, source database, models, or scenes.

MOLECULE WORLD PRO

Pro adds tools for creating and saving molecular content.

Selections: select residues in the sequence, search by variant, range, or motif, select residue neighbors, then style, color, hide, and lock them.

Scenes: save named views, including selections, styles, and camera position, inside the structure file. Step through scenes to guide an exploration or create a presentation.

Model sets: superimpose structures and compare how closely they align. Compare experimental structures, predicted models, variants, or alternative conformations, and save the model set and its comparison data for sharing.

Collections: package structures, models, scenes, and descriptions into a single file. Hide selected structures for exercises and optionally lock the collection for distribution.

Pro also includes undo and redo and high-resolution image capture. It is a single in-app purchase with no subscription and can be shared with Family Sharing.

TEACH SEQUENCE, STRUCTURE, AND FUNCTION

Build collections around a biological question. Give students related structures, variants, or predicted models and let them investigate the differences themselves. Use scenes to guide an exploration, hide structures for unknown-structure exercises, and move between aligned sequence and 3D structure to connect sequence changes with their structural consequences.

Everything created with Pro opens in the free Molecule World viewer on iPhone, iPad, and Mac. Students and colleagues can explore collections, step through scenes and model sets, change views, and save images for assignments and presentations.

BUILT FOR THE APPLE ECOSYSTEM

Molecule World runs as a unified app on iPhone, iPad, and Mac. Optional iCloud support keeps your library available across devices.

Molecule World is developed by Digital World Biology LLC, with support from National Science Foundation awards IIP 1315426 and DUE 2055036.

Version History Molecule World 5.0 brings sequence, structure, prediction, and comparison together in a molecular workspace for exploring proteins, DNA, and RNA.

Explore experimentally determined structures alongside computationally generated models, including structures predicted from sequence. Compare normal and mutant proteins, examine alternative conformations, and investigate how sequence changes affect 3D structure.

Molecule World Pro on iPad adds tools for creating reusable molecular explorations. Select residues by sequence, variant, range, motif, neighborhood, or binding interface. Style and color what matters, hide what does not, and save the result as a named scene. Superimpose structures into model sets and compare their alignment, both overall and by chain. Package structures, scenes, and descriptions into collections that can be shared with students or colleagues.

The free Molecule World viewer on iPhone now opens these Pro-created collections, scenes, and model sets. Explore molecular structures on iPhone, including superimposed models and saved views created on iPad.

SEQUENCE + STRUCTURE

The sequence viewer connects aligned sequences directly to the 3D structure. Compare copies of a molecule, examine mutations, and read aligned models down the same residue columns.

SCENES

Save a molecular view—including selections, styles, and camera position—inside the structure file. Step through scenes to guide an exploration or presentation.

MODEL SETS

Superimpose up to 20 structures and compare how closely they align, both overall and by chain. Compare experimental structures, predicted models, variants, or alternative conformations in the same workspace.

COLLECTIONS

Package related structures into a single file with descriptions and an ordered sequence of models and scenes. Hide selected structures for exercises and optionally lock the collection for distribution.

FREE ON EVERY DEVICE

Everything created with Pro opens in the free Molecule World viewer on iPhone, iPad, and Mac. Students and colleagues can explore collections, step through scenes and model sets, change views, and capture high-resolution images without needing Pro.

Molecule World 5.0 makes it easier to explore how sequence, structure, and function are connected—from individual structures to collections of models and guided molecular experiences. 5.0 Oct 5 Crystallographic waters can now be displayed with the new "All + water" option under Show. It's off by default and available whenever a structure includes
water.

Conserved domains for every format. Domain coloring used to require an MMDB or Cn3D file. It now works with PDB, mmCIF, and BinaryCIF structures too, with
domain names looked up from NCBI's Conserved Domain Database. Lookups on large assemblies are much faster with full domain names.

This release also includes improvements in how metal ions and other atoms are displayed in the color key, secondary coloring in very large structures, residue displays in nucleic acids ribbons, and other fixes. 4.6 Aug 2 New in 4.5:

- New layout on Mac and iPad to support sequence viewing.

- Sequence view (iPad & Mac) — Tap Sequence at the bottom of the screen to see each chain's protein, DNA/RNA sequences, and heterogens, colored to match your current view. Scroll with the arrow keys, mouse drag, or scroll wheel.

- Better keyboard support — Move through your file list with the arrow keys, and open a structure with Shift (Mac) or Return (iPad) — works with search results too.

- Search that sticks — Your search term now stays put while you browse, just like folders already do, and clears when you quit and relaunch.

- Visual polish and an updated in-app Help and other improvements.

This version also includes everything from previous releases:
- Full 3D visualization — rotate, zoom, and pan through proteins, DNA, RNA, and small molecules

- Multiple representation styles — ball-and-stick, space-filling, tubes, ribbon/cartoon, molecular surfaces, and wire mesh

- Focused selections — show just proteins, nucleic acids, ligands, backbones, or alpha-carbon traces

- Scientific color schemes — by element, chain, residue, secondary structure, charge, hydrophobicity, domain, and B-factor

- Fetch structures directly from the Protein Data Bank, PubChem, and NCBI by ID or keyword

- iCloud sync keeps your library — and your place in it — consistent across iPhone, iPad, and Mac

- Clear, context-aware legends that explain exactly what you're looking at

This version is a cosmetic app store fix that resolves an issue where a portrait orientation screen capture broke the iPad display. 4.5.1 Jul 19 New in 4.5:

- New layout on Mac and iPad to support sequence viewing.

- Sequence view (iPad & Mac) — Tap Sequence at the bottom of the screen to see each chain's protein, DNA/RNA sequences, and heterogens, colored to match your current view. Scroll with the arrow keys, mouse drag, or scroll wheel.

- Better keyboard support — Move through your file list with the arrow keys, and open a structure with Shift (Mac) or Return (iPad) — works with search results too.

- Search that sticks — Your search term now stays put while you browse, just like folders already do, and clears when you quit and relaunch.

- Visual polish and an updated in-app Help and other improvements.

This version also includes everything from previous releases:
- Full 3D visualization — rotate, zoom, and pan through proteins, DNA, RNA, and small molecules

- Multiple representation styles — ball-and-stick, space-filling, tubes, ribbon/cartoon, molecular surfaces, and wire mesh

- Focused selections — show just proteins, nucleic acids, ligands, backbones, or alpha-carbon traces

- Scientific color schemes — by element, chain, residue, secondary structure, charge, hydrophobicity, domain, and B-factor

- Fetch structures directly from the Protein Data Bank, PubChem, and NCBI by ID or keyword

- iCloud sync keeps your library — and your place in it — consistent across iPhone, iPad, and Mac

- Clear, context-aware legends that explain exactly what you're looking at 4.5 Jul 17 This update brings faster ways to open and explore structures, especially on Mac.

Keyboard controls — On Mac and iPad with a keyboard, use the arrow keys to rotate, Option+arrows to pan, and ⌘+ / ⌘− to zoom. Hold a key for continuous motion.

Drag and drop (Mac) — Drag a structure file from Finder straight onto the 3D view to open it. Works with PDB, CIF, BCIF, MMDB JSON, CN3, and SDF files, including gzipped and zipped.

Windows and tabs (Mac) — Right-click a structure to open it in a new window or tab, so you can compare structures side by side.

Folder counts — Folders now show how many structures they contain, and the count updates as you browse and filter.

Better PubChem search — Search by compound name, molecular formula, or SMILES, with support for wildcards and multi-term queries.

Plus refinements to in-app Help and various fixes. 4.2 Jul 13 MoleculeWorld 4.1
Mac support, new visualization options, and a faster app.

Now available on Mac — your library and Pro unlock carry over automatically via iCloud.

New Wire Surface mode — the molecular surface as a wireframe mesh, so you can see structure detail through the surface shape.

New B-factor coloring — a blue-white-red gradient that highlights areas of higher atomic motion or uncertainty, scaled to each structure.

Faster loading for large structures, especially big assemblies.

Bug fixes and stability improvements.

This release builds on :
- iCloud sync to keep your structures on all your devices

- Smoother, higher-quality ribbon and surface rendering

- Domain-based coloring that reveals how a structure is organized

- Sugar (glycan) residues colored by standard SNFG conventions

- Clearer annotations for modified nucleotides 4.1 Jul 6 Molecule World is back — completely rebuilt for iPhone, iPad, and Mac.

This release brings:
- iCloud sync to keep your structures on all your devices
- Smoother, higher-quality ribbon and surface rendering
- Domain-based coloring that reveals how a structure is organized
- Sugar (glycan) residues colored by standard SNFG conventions
- Clearer annotations for modified nucleotides

More is on the way. 4.0 Jul 2 Fixed problem with downloading collections. 3.10 10/17/2020 Fixed hydrophobicity coloring for proline. 3.07 05/21/2018 Fixed alanine hydrophobicity coloring, increased allowed number of atoms to support larger structures 3.0.6 05/02/2018 Minor bug fixes. Fixed bugs that caused crashes related to the new NCBI structure format. 3.0.5 03/06/2018 Updated for iOS 10, fixes minor bug in displaying structures immediately after downloading from the MMDB (NCBI) or from the PDB. Also fixes minor bug in displaying PDB files when downloaded from website. 3.0.2 11/08/2016 - Download individual structures and entire collections of molecules to support teaching activities
- Lock a chain to prevent changes in appearance
- Performance improvements make rendering faster and improve behavior with larger structures

If you enjoy using Molecule World, leave us a review – it really helps! 3.0 07/18/2016 Minor bug fix to correct problem with downloading files from the PDB. 2.2.1 05/04/2016 - Color and draw proteins to show secondary structure elements (beta sheets, alpha helices, and coils)
- Use the color key to identify secondary structure elements
- Improved ability to search for sequences
- Added ability to use a wild card character (*) in a sequence search
- Improved rendering for large structures like antibodies, that download as alpha carbons.
- View a wider range of PDB files.
- Added ability to show thorium
- Fixed a bug where alpha carbon structures were not displayed on initial download 2.2.0 10/23/2015 New rendering styles: backbone view with side-chains hidden, backbone view with oxygens hidden
Identify binding sites for other molecules, drugs, or small chemicals by selecting nearby residues
Search and select sequences by pattern or one letter code
Use mixed drawing and coloring modes
Improved coloring for smaller chemicals (water, glucose, etc.) 2.1.0 03/10/2015 - An adaptive sequence viewer displays DNA, RNA, and protein sequences and other chemicals
- Protein, DNA, or RNA chains, single residues, and other chemicals (coenzymes, metals, or drugs) can be selected and highlighted from the sequence viewer
- The sequence viewer allows any object in a structure to be highlighted, dimmed, or hidden
- Rainbow coloring shows where amino acids or nucleotides are located within a chain and helps illustrate protein and RNA folding
- Instant recoloring from the visualization menu
- Expanded information view
- Improved display of bonds to metals, drugs, and disulfide bonds
- Improved search
- Structures are now downloaded from the NCBI (MMDB) as biological units
- Structures from the PDB are downloaded as asymmetric units
- View large, complex, structures (< 120,000 atoms)
- Minor bug fixes 2.0.0 12/16/2014 Minor updates to support iOS8 1.1.1 10/08/2014 - Modified adaptive color key to support residue mode
- Added Apply Change button
- Improved handling of image files
- Compensated for changes in downloading PDB files
- Minor bug fixes 1.1 09/14/2014 - Improved depth properties increase the 3 dimensional quality of molecular structures and allow users to zoom in to a greater extent.
- Some bond rendering issues have been fixed.
- Performance has been improved for large molecules.
- Minor improvements have been made to the interface. 1.0.1 05/27/2014 1.0 04/29/2014