RxCubed documentation
How RxCubed works, what each tool calculates, and the drug-discovery background behind it. Free to read — no account needed.
Get started (4)
- What RxCubed isA plain-language overview of the workspace, its navigation, and how evidence is organised.
- DashboardThe project home page and a plain-language view of research progress.
- AI AssistantWhat the assistant can do, how to ask it well, and how RxCubed keeps the cost of using it down.
- You ask, we build itThis is how RxCubed gets built. Here's how to ask.
Tutorials (1)
Scientific concepts (1)
Find papers (1)
Collect files (9)
- File CollectionCollect structures, sequences, compounds, and other files from supported databases.
- RCSB PDBSearch experimental structures in the RCSB Protein Data Bank.
- UniProtSearch curated protein records — sequence, function, features, and cross-references.
- AlphaFold DBCollect predicted protein structures and their per-residue confidence.
- PubChemCollect small-molecule records — structure files and basic chemical properties.
- ChEMBLCollect measured bioactivity — what a compound actually did against a target, in a real assay.
- InterProCollect protein family, domain, and functional-site annotations.
- Viewers and filesOpen saved files, inspect evidence, and understand missing-file status.
- 3D Structure ViewerInspect saved PDB and mmCIF structures in the Mol* viewer.
Model (3)
- ModelSelect and run computational tools, then inspect their outputs and provenance.
- Tool SelectorFind a computational tool by name, provider, modality, or category.
- Filling in a tool and collecting its resultsHow to set file and text inputs, check a file before using it, find a file you don't have yet, and collect results from runs that take time.
Results Hub (3)
Create reports (2)
Settings and services (1)
RxCubed tools (26)
- RxCubed ToolsComputational tools that run on RxCubed with no external provider key.
- Binding affinityPredicts the binding free energy and dissociation constant for the interface between two sets of chains in a complex, using PRODIGY. Use to compare how tightly related complexes bind. It assumes the complex is real and says nothing about whether two proteins interact.
- 3D conformer generationGenerates one 3D starting geometry for a compound saved flat (e.g. a PubChem download), using either RDKit or Open Babel. Use before docking, or anywhere a 3D structure is needed and only a 2D one exists.
- Contact mapper (geometric)Lists which residues of a chain touch a binding partner, by geometric distance, in both PDB and UniProt numbering.
- Contact mapper (chemical)Types every contact between a chosen partner (a chain or a ligand) and the rest of a structure — hydrogen bond, salt bridge, aromatic stacking, hydrophobic — using Arpeggio's implementation of the CREDO interaction rules. Use alongside Contact mapper (geometric) when the chemistry of an interface, not just its geometry, is the question.
- Drug-likeness filtersRuns a compound through Lipinski's rule of five, Veber's rule, and PAINS, returning one pass/fail verdict per rule set. Use as the routine first-pass triage on a candidate before carrying it further.
- Format conversionConverts a structure between SDF, PDB, mmCIF, MOL2 and SMILES, with nothing invented — no 3D coordinates generated, no geometry changed. Use when a downstream tool or an external program needs a different file format than what's saved.
- Hydrogen-bond persistenceWhich protein-ligand hydrogen bonds hold through a Molecular dynamics trajectory, and for how much of it — whether a bound complex is stable at the interface.
- Local structure agreementCompares two structures of the same protein without superposing them first (lDDT), so one badly-modeled region can't distort the score the way it can with a global alignment. Use to score a predicted structure against a reference, or to see exactly which regions of two structures actually disagree.
- Ligand extractionPulls a bound ligand out of a PDB or mmCIF entry as its own SDF, with correct bond orders when you supply the compound's SDF as a template. Use when you have an experimental protein–drug complex and need the drug on its own — to draw a docking box around the real binding site, or to measure docked poses against the crystal pose.
- Molecular dynamicsRuns a real GROMACS simulation on a structure, optionally with a bound ligand, and produces a trajectory the platform's own analysis tools can read directly.
- Molecular propertiesComputes the standard small-molecule property profile — molecular weight, LogP, TPSA, hydrogen-bond donors and acceptors, rotatable bonds — from a saved compound structure. Use for a first read on a candidate before ADMET or drug-likeness screening.
- Pocket detectionFinds candidate binding pockets on a structure and ranks them by score and druggability, giving each a centre and a box you can dock into. Use when you have a structure and need somewhere to dock, or want to know whether a protein has a site a small molecule could occupy at all.
- Pose RMSDMeasures how far docked poses sit from a reference pose, in Ångström, symmetry-corrected and without superimposing. Use it to check whether a docking setup can reproduce a binding position that is already known — the standard way to decide whether to trust docking results on a target at all.
- Secondary structureAssigns helix, strand and coil to every residue of a structure using DSSP, reported as contiguous elements like "helix, A12-A24". Use to describe a fold, compare two structures' architecture, or find which regions are ordered before trimming or modelling.
- Sequence alignmentAligns two or more protein sequences and reports percent identity between them. Use to judge whether one protein is a usable template for another, to find conserved positions, or to check how similar two family members really are.
- Similarity searchRanks a set of candidate compounds by fingerprint similarity to one query compound, using Tanimoto similarity over a Morgan or MACCS fingerprint. Use to find which of several saved candidates is closest to a reference structure, or to triage a batch of hits.
- Small-molecule generationProposes new candidate molecules by extending a seed compound at an open valence, using CReM over a real ChEMBL fragment database. Use to propose a scaffold nobody has drawn yet, when Similarity search's existing library isn't enough.
- Small-molecule linkingJoins two seed compounds with a fragment-database-sourced linker, using CReM over a real ChEMBL fragment database. Use for fragment-based drug discovery — combining two smaller candidates into one, not extending or modifying a single lead.
- Small-molecule optimizationProposes alternatives to part of a seed compound — a candidate that could bind where the original does, not a bigger version of it — using CReM over a real ChEMBL fragment database. Use once a lead already exists and the question is "what else could work here."
- Small-molecule screeningGenerates candidates from a seed compound and docks them one at a time against a receptor until enough actually beat a real affinity bar. Use once a receptor exists and the question is "which of these would actually work," not just "which of these look drug-like."
- Structure alignmentCompares two structures and reports TM-score and RMSD, to judge whether one can stand in for the other.
- Structure cleanupFills in missing residues and atoms, replaces nonstandard residues, adds hydrogens at a chosen pH, and optionally strips waters/ligands, via PDBFixer. Use to prep a structure before docking or simulation, especially one pulled straight from a crystal structure.
- Structure predictionPredicts a 3D structure directly from a sequence (OmegaFold) — no template, no MSA, no reference structure needed. Capped at 274 residues.
- Surface accessibilityMeasures how exposed each residue is to solvent, as an absolute area and as a fraction of that residue type's maximum. Use to tell surface from buried before choosing mutation sites, to find an exposed patch, or to see which residues a partner would cover.
- Trajectory stabilityRMSD-over-time, per-residue flexibility, and radius of gyration for a Molecular dynamics trajectory — whether a structure stayed stable, and which regions moved.