Catalophore Pro
The Molecular Intelligence Platform

Your whole protein library, one searchable workbench.

Catalophore Pro brings every structure, sequence, cavity, ligand and experiment into one place, then lets you search millions of binding sites by shape and physico-chemical property, run modelling and docking on your own compute or in the cloud, your choice, and hand the results to your team as a branded report. Whether you can test 10 or 10 million candidates in the wet-lab, you always have to decide where to draw the line in-silico. Catalophore Pro is the ranker that draws it for you, with the structural evidence to defend the cut.

catalophore-pro · platform dashboard
Catalophore Pro platform dashboard with tiles for Fridge, In-Silico Experiments, Projects, Running Jobs, Collaborations and a live activity feed

Catalophore Pro home. One workspace for your whole molecular library: structures, sequences, cavities, ligands, projects, jobs and collaborators. Every action audited, every run reproducible.

10.2 MBinding sites indexed, searchable by physico-chemical property
231 kPDB structures, every chain and biological assembly parsed
574 kSwiss‑Prot entries mirrored locally, ready for offline lookup
On‑premRuns on your site. No internet access needed.
01 · The Workflow

From a sequence or structure to a ranked shortlist, in one platform.

Catalophore Pro covers the entire path from raw data to a defensible decision in one workbench. Each stage hands the next exactly what it needs, and every step is reversible, shareable and traceable.

Ingest

Library

Upload structures, pull from PDB or AlphaFold DB, import sequences from UniProt.

Detect

Cavities

Every binding site as a 3D point cloud with 30+ physicochemical property fields.

Match

PCCS

Search the cavitome for shape and physico-chemical property similarity, not just sequence.

Score

Statistics

BLAST-style ranking with real Gumbel e-values. Interpretable. Defensible.

Decide

Report

Branded PDF / DOCX / XLSX / PPTX with a UUID watermark. Hand it to the lab.

02 · One library, every type

All your molecular data in one place. Browseable. Filterable. Yours.

Structures, sequences, cavities, ligands, peptides, nucleic acids and assemblies. Every asset lives behind the same powerful browser, with list / cards / images views, advanced filters and saved presets.

Every asset, one browser

Eight asset types, one UX

PDB structures, custom uploads, computed models, sequences, cavities, ligands, peptides, nucleic acids and biological assemblies. Same search, same filters, same export.

Counts that matter

Populated, not promised

Up to 10.2 M cavities and 231 k PDB structures indexed today, steadily growing. Each Catalophore Pro system can be tailored to the libraries your programs actually need.

No vendor lock‑in

Everything exports

PDB, CIF, FASTA, MOL2, branded PDFs, full project bundles. Your data stays yours, in formats your downstream tools already speak.

catalophore-pro · fridge overview
Catalophore Pro Fridge Overview showing live counts for Protein Cavities, PDB Structures, Protein Sequences, Custom Structures, Homology Models, Ligands and PISA assemblies

Fridge Overview. Every molecular asset in one place, with live counts and a single search bar.

Let your precious data grow with you. Don’t let it bury you in the age of generative AI. Every structure you upload, every experiment you run and every annotation you add stays indexed, searchable and connected, so the value of your library compounds rather than rotting in a shared drive.
03 · The cavitome, at platform scale

10.2 million binding sites, every one indexed as a physico-chemical point cloud.

Most platforms hand you a search box and a few PDBs. Catalophore Pro hands you a populated, queryable cavitome: every binding pocket pre-detected from 231 k PDB structures and your own uploaded structures, all stored as 3D point clouds with property channels per grid point. Submit a query cavity and rank the whole catalog in one experiment.

  • Cavity Search. Submit any structure, get every druggable pocket back as a first-class object you can browse, share and re-use. Tunable pH, configurable grids.
  • PCCS Cavity Matching. Iterative Closest Point matching with property-weighted scoring across the whole library. Ranked, statistically scored, exportable.
  • 21 property channels today, growing toward 30+. Per grid point: hydrophobicity, electrostatics, desolvation, H-bond donor and acceptor specialisations, aromatic and cation-pi interactions, accessibility, flexibility, chain context, and the full heavy-atom stack down to the halogens. Every channel is a tunable weight.
  • Halo point clouds. A complementary outward-facing point cloud that reaches past the protein surface into the surrounding space, mapping the physico-chemical environment where protein-protein and protein-peptide binding partners approach. Search surface interaction sites, not just internal pockets.
  • Storage that scales. Searching across millions of cavities stays fast on commodity hardware, with no exotic infrastructure required.
catalophore-pro · cavities
Protein Cavities browser in cards view, each card showing the parent structure, cavity index, volume and point count

Protein Cavities, cards view. Same list, every pocket as a card with its key metrics. List, cards and images views ship with every fridge.

04 · Decisions you can defend

Explainable outcomes. We love AI so that you don’t have to.

AI is guidance. You are the decision maker. Catalophore Pro scores every match with a documented physico-chemical similarity formula and a Gumbel-distribution e-value, exactly like BLAST does for sequences, so a hit you take to your VP, your IP team or a regulator is interpretable and defensible. AI joins the workflow where it earns its place: structure prediction, paper extraction, natural-language navigation. Every output points back to the physico-chemical evidence behind it, and the decisions stay yours.

  • Documented formulas. flat_score and importance_score scaled by voxel volume. The math is public.
  • Per-property weights. Hydrophobicity, polarity, charge, pi-pi, cation-pi, metal coordination, desolvation, ligand-site fit. Every property is a tunable knob.
  • Reproducible. Every run has a UUID. Every report cites it. Every change is in the audit log.
catalophore-pro · matching results
Catalophore Pro PCCS matching results table with per-target similarity, query and target coverage and per-property breakdown

Matching Results. Every hit ranked by physico-chemical similarity with a full property-by-property breakdown.

“We love AI so that you don’t have to.” Catalophore Pro uses physico-chemical methods, point clouds and AI, and tells you which one made the call, so the human stays the decision maker.
05 · Build, mutate, dock

Choose your method. We support all of them.

Need a structure? Fetch it from AlphaFold DB, predict it with ESMFold, AlphaFold2 or OpenFold, or build it the classical way with template-based homology modelling. Need a pose? Run AutoDock VINA against a cavity, or DiffDock if you want AI-generated poses. Mutate residues in silico with combinatorial expansion across chains. We curate the best methods in the field and wire them into the platform for you, so you pick the approach and we handle the rest.

Detect

Cavity Search

Find every binding site in a structure, configurable by pH. Outputs first-class cavity objects you can browse and re-use.

Compare

Cavity Matching (PCCS)

Shape and physico-chemical property similarity across the full library. Ranked, scored, exportable.

Dock

Molecular Docking

AutoDock VINA against any cavity. Scored, clustered, every pose downloadable as PDB / PDBQT / PSE.

AI Dock

DiffDock

Diffusion-based pose generation with confidence scoring, for when you want AI to do the hard sampling.

Predict

Model Builder

AlphaFold DB · ESMFold · AlphaFold2 · OpenFold · classical template-based homology modelling · PSI-BLAST. All in one form.

Engineer

Mutator

Combinatorial in-silico mutations across chains, with energy minimisation. Parse a notation, get a library.

Don’t know which method is right for your protein family or your reaction? Let us fiddle around to find the best bioinformatics methods for your use case. Our team experiments alongside yours, so you don’t have to figure out the optimal pipeline from scratch.
catalophore-pro · experiments
Catalophore Pro Experiments dashboard with tiles for Cavity Search, Mutator, Model Builder, Cavity Matching, Molecular Docking, DiffDock and forthcoming Dynamics, Affinity and Folding

Experiments. Every algorithm in one dashboard: Cavity Search, Cavity Matching, Model Builder, Molecular Docking, DiffDock. Dynamics, Affinity and Folding shipping next.

06 · Projects & collaboration

Workspaces your team actually uses.

Group anything (structures, sequences, cavities, experiments, files) into named projects. Invite by email, assign roles, share at item or project level. Built for teams that need to move fast without losing track of who did what.

Group

Projects

Bundle the structures, sequences and experiments behind a hypothesis. Invite collaborators with viewer / editor / owner roles. Item-level overrides when you need them.

The heart of every experiment

Collections

Collections are how you tell an experiment what to run against. Hand-pick cavities, structures or sequences, save them as a Collection, then point Cavity Matching, Docking or any other experiment at it. Filters can be promoted into Collections; Collections can be shared, versioned and re-used across runs. Nothing in Catalophore Pro runs at scale without them.

Comply

Auditable & GDPR-ready

Full audit log of every action, ~45 granular permissions, one-click user data export, encrypted API keys, CSRF protection out of the box.

catalophore-pro · custom structures
Catalophore Pro Custom Structures browser in images view, a gallery of rendered structure thumbnails

Custom Structures, images view. The same library, every uploaded structure rendered to a thumbnail. Switch to list when you need columns, cards when you need both.

Every upload, every mutation, every run, traceable.

Custom structures don’t get lost. They carry their parent, their mutations, the experiment that produced them, and the project they belong to, from upload through report.

  • Provenance built in. Every row knows where it came from and what was done to it.
  • Mutation tracking. A6V, M17L, S25T. Parsed, indexed, searchable.
  • Experiment lineage. See the run that produced any custom structure, jump to its result page.
07 · Cavi, the AI assistant

Chat with your data. Hand it a paper, get a project.

Cavi is the platform’s chat assistant. It can answer questions about your library, kick off cavity searches, build a Project from a DOI, run Python in a sandboxed notebook to plot your results and write you a branded report, while every action that touches your data is previewed and explicitly confirmed.

Paper → Project

One DOI, one project

Drop a DOI in chat. Cavi extracts UniProt IDs, PDB codes and mutations from the abstract and offers to build a full project (sequence import, AlphaFold lookup, cavity search) in one click.

40+ wired skills

Never invents an operation

Cavi picks from a server-side registry of skills. Every write is previewed and confirmed. Every action lands in the audit log.

Your LLM, your rules

Bring your model

Anthropic, Google, OpenAI, Abacus.AI or a local Ollama / Gemma model. Off by default. Toggleable per facility.

08 · Branded reports

One click to a report your IP team will accept.

Every experiment, every project, every structure detail page can become a branded report with your logo and footer, a UUID watermark and a “what’s new since last report” diff, in the format your team prefers.

  • PDF, DOCX, XLSX, PPTX. Same content, your team’s preferred format.
  • Your logo, your colors. Header and footer branding configurable per facility.
  • UUID watermarks. Every report cites the exact run ID. Reproducible by definition.
  • Diff since last run. “What’s new since last report” baked in.
  • Auto-embeds. Structure images, sequence listings, cavity matches, docking poses, all rendered.
catalophore-pro · cavity search experiment
Catalophore Pro cavity search experiment detail page with progress, results table, project bindings and metadata, ready to export as a branded report

Experiment detail. Settings, results, project bindings, metadata, ready to render as a branded report in one click.

09 · Built for on‑prem from day one

Your idea. Your data. Your IP. Our platform.

Catalophore Pro is built for pharma-grade deployment from day one. The whole stack runs on your site: web UI, job scheduler, gateway, fileserver, license authority, workers, and the database itself. Reference data (Swiss-Prot mirror, PDB mirror, ligand libraries) ships pre-loaded. All on your site, no internet access needed to run. Submit jobs to your existing HPC clusters, Docker hosts and GPU nodes from the same UI; worker health, mount validation, license quotas and stall detection are all monitored.

Deploy

Self-hosted

One tarball, one Docker compose. No SaaS dependency, no shared tenancy. Your facility is yours.

Compute

HPC, Docker & GPU

Connect your existing HPC clusters, Docker hosts and GPU nodes as Facilities. GPU-accelerated folding when you have the silicon for it.

Air-gap

Offline-first

574k UniProt entries, full PDB mirror, ligand libraries, all local. No internet access needed at runtime. Full air-gap deployments supported.

Integrate

Plug into your workflow

Documented REST API mirrors every UI action. Drop it into your Snakemake / Nextflow / KNIME / internal Python pipelines. Cavi-side MCP support for agent integration.

Flexible plans

Grow with us. From a single-team pilot to enterprise rollout.

Catalophore Pro is built to scale across the org chart, not just the data. Start with a single team and a focused use case; extend to your wider discovery group; deploy enterprise-wide with multiple Facilities, custom branding packages and role-segregated access. Same platform, same workflows, same data model. No migration tax.

Start small

Single-team pilot

A handful of users, one Facility, your existing structures and ligands loaded. Up and running in a single sprint, no commitments beyond it.

Scale up

Discovery group

Add seats, projects, shared collections, multi-team RBAC, more Facilities for HPC and GPU. Branded reports start carrying your logo.

Enterprise

Org-wide rollout

Per-facility branding packages (CATALObase, CavitOmiX, your own), federated RBAC, automated backups, archival lifecycle, full audit reporting for compliance.

For biotech and pharma teams

From a new product idea to the lab capacity you actually need.

Every year your team is handed millions (and now, with AI-folded proteomes, billions) of new structural datapoints. No matter how many candidates you can score in silico, the assay plate only fits so many. Catalophore Pro is the ranker that turns that flood into a defensible cutoff: the top N your team takes to the bench.

A defensible ranked cutoff, not a 10,000-row CSV.

A discovery scientist has a target. The platform pulls every related PDB entry and every computed model, detects the binding sites, and ranks the cavities by their physico-chemical similarity to a known ligand pocket. Ten candidates, scored with real statistics, with the structural rationale attached, not ten thousand. Got more wet-lab capacity? Push the cutoff out. The next hundred are exactly the kind of non-obvious hits sequence homology never surfaces, the ones that turn into your next patent or your next FTO position.

A protein engineer has a reaction. The platform searches the cavitome for sites that match the geometry and physico-chemical properties the reaction needs, returns enzymes from folds you’d never have queried by sequence, and lets you mutate the best ones in silico before a single tube leaves the freezer.

An IP team has a question. Every hit cites a UUID, a scoring formula, a property breakdown and an audit-logged run. The report lands as a branded PDF with your logo on top. Defensible by construction.

Net effect: success rates go up because the candidates you advance are the ones the structural evidence actually supports, and your lab capacity goes to the experiments most likely to work.

Get started

Put Catalophore Pro to work.

Two ways to start: a guided demo on your own protein, or a conversation about on-prem deployment, API access and custom facility setup.

Book a demo

Send us a PDB ID, a UniProt ID or a sequence. We’ll run it through Catalophore Pro on a live instance and walk you through what the platform finds.

Book a demo

Talk integration

On-prem deployment, GPU facilities, REST API access, custom branding packages, or a connector to your existing pipeline. Let’s scope it.

Talk integration

Questions? Write to customer@innophore.com · Built and maintained by Innophore, Graz, Austria.