---
title: Job Types Catalog
description: >-
  Searchable catalog of computational biology tools with categories and typical
  runtimes
tags:
  - reference
  - tools
  - catalog
---
The Job Types Catalog is the reference list of every computational tool you can run on the platform, grouped by category with its compute profile and typical runtime. Reach for it when you're deciding which tool fits your task or need a tool's exact name before submitting. Each entry can be invoked through the [REST API](/docs/api/rest-jobs), the [SDK](/docs/api/sdk-jobs), or the [Harness](/docs/api/sessions-execute).

  beginner
  10 min

## Job Types Catalog

Complete catalog of computational tools available on the IvyAI platform. Each tool can be invoked via the [REST API](/docs/api/rest-jobs), [SDK](/docs/api/sdk-jobs), or [Harness](/docs/api/sessions-execute).

---

## Structure Prediction

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `esmfold` | ESMFold protein structure prediction | GPU | 30s–5min |
| `esm3_generate` | ESM3 protein generation | GPU | 1–3min |
| `esm3_inverse_fold` | ESM3 inverse folding (structure → sequence) | GPU | 30s–2min |
| `esm3_embeddings` | ESM3 protein embeddings | GPU | 15–45s |
| `colabfold` | ColabFold MSA-based structure prediction | GPU | 2–15min |

---

## Molecular Docking & Design

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `diffdock` | DiffDock protein-ligand docking | GPU | 1–5min |
| `gnina` | GNINA CNN-scored docking. **Retired:** use `diffdock`, then rescore with MM-GBSA | GPU | — |
| `colabdock` | ColabDock flexible docking. **Not currently callable:** its AlphaFold2 model weights are missing | GPU | — |
| `smart_dock` | SmartDock consensus docking | GPU | 3–8min |
| `reinvent4` | REINVENT4 de novo molecule generation | GPU | 5–30min |
| `genmol` | GenMol molecular generation (SAFE native) | GPU | 2–10min |
| `denovo` | De novo drug design | GPU | 5–20min |

---

## Property Prediction

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `admet_ai` | ADMET property prediction | CPU | 10–30s |
| `admetlab3` | ADMETlab3 comprehensive ADMET profiling | CPU | 15–45s |
| `graphsol` | GraphSol aqueous solubility prediction | CPU | 10–20s |
| `deepsol` | DeepSol deep learning solubility. **Not currently callable:** disabled upstream (protobuf incompatibility); use `graphsol` | CPU | — |
| `protox3` | ProTox-3 toxicity prediction. **Retired:** use `admet_ai` for the overlapping endpoints | CPU | — |
| `deeppurpose` | DeepPurpose drug-target interaction | GPU | 30s–2min |

---

## Database Screening

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `rdkit_full` | RDKit SMILES validation and molecular properties | CPU | 5–15s |
| `zinc` | ZINC database compound screening | CPU | 10–30s |
| `pubchem` | PubChem compound queries | CPU | 5–15s |
| `pubchem_substructure` | PubChem substructure search | CPU | 10–30s |
| `chembl` | ChEMBL bioactivity database search | CPU | 10–30s |

---

## Sequence Analysis

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `blast` | BLAST sequence homology search | CPU | 10s–2min |
| `biotite_fetch` | UniProt/PDB structure fetching | CPU | 5–15s |
| `aizynthfinder` | AiZynthFinder retrosynthetic route planning | CPU | 30s–5min |

---

## Fragment & Scaffold Design

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `fragment_growing` | Fragment-based drug design. **Retired:** no replacement | GPU | — |
| `fragment_library` | Fragment library management. **Retired:** no replacement | CPU | — |
| `fragment_search` | Fragment discovery and search | CPU | 10–30s |
| `fragment_extract` | Fragment extraction from structures | CPU | 10–30s |
| `scaffold_decoration` | Scaffold decoration with R-groups | GPU | 2–10min |
| `linker_design` | Linker design between fragments | GPU | 2–10min |
| `motif_extension` | Motif-based molecule extension | GPU | 2–10min |

---

## Literature & NLP

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `biobert_pubmed` | BioBERT scientific literature mining | GPU | 15–45s |

---

## Protein Preparation

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `pdb2pqr` | Protonation state and charge assignment (PDB2PQR + PROPKA) | CPU | 15–30s |
| `p2rank` | Binding pocket detection (P2Rank) | CPU | 30s–2min |

Protein preparation is these two job types, the same ones the chat interface runs (`pdb2pqr_protonate`, `p2rank_predict`). `pdb2pqr` takes inline structure text (`pdb_content`); `p2rank` takes `pdb_content`, a `pdb_id` or a `uniprot_id`. There are no `proteinprep*` job types, and no structure-quality job.

---

## Regulatory & Safety

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `drugcentral_regulatory` | DrugCentral regulatory approvals lookup | CPU | 5–10s |
| `chembl_drug_warnings` | ChEMBL drug warnings and withdrawals | CPU | 5–10s |
| `pubchem_regulatory` | PubChem regulatory data (DEA, ATC) | CPU | 5–10s |

---

## Genomics & Databases

| Tool | Description | Compute | Typical Runtime |
|------|-------------|:---:|:---:|
| `encode_search` | ENCODE database functional genomics search | CPU | 10–30s |
| `string_network` | STRING protein-protein interaction networks | CPU | 10–30s |
| `uniprot_search` | UniProt protein database search | CPU | 5–15s |
| `pdb_search` | RCSB PDB structure database search | CPU | 5–15s |

---

## Analysis Levels

All tools support three analysis levels that control the depth of result processing:

| Level | Description |
|-------|-------------|
| `basic` | Fast results with standard output only |
| `standard` | Balanced analysis with key quality metrics (default) |
| `comprehensive` | Full analytical suite with extended result fields |

### Example

```ts
await ivy.jobs.submit({
  toolName: "esmfold",
  parameters: { protein_sequence: "MKFLILLFNILCLFPVLAADNH" },
  analysisLevel: "comprehensive", // Full pLDDT breakdown, per-residue scores, etc.
})
```

---

## Guest-Accessible Tools

Callers with no key reach an allowlisted guest catalog through the keyless orchestrate request, not by submitting a job type directly. See [Guest curl](/docs/api#guest-curl) for the request and its limit.

---

## Programmatic Tool Discovery

### Harness API

The web app serves the tool registry at `/api/harness/tools`:

```bash
# List tools with filtering
curl "https://www.ivybiosciences.com/api/harness/tools?category=docking&maxCost=standard" \
  -H "Authorization: Bearer ivy_your_key"

# Get specific tool details with JSON Schema
curl https://www.ivybiosciences.com/api/harness/tools/diffdock \
  -H "Authorization: Bearer ivy_your_key"
```

### SDK (planned)

`@ivybiosciences/sdk` is a planned specification, not a released package. Today, list tools with the REST calls above or `ivybloom` in the [CLI](/docs/cli).

```ts
import { JOB_TYPES } from "@ivybiosciences/sdk"
import type { JobType } from "@ivybiosciences/sdk"

// All registered tool names
const tools = Object.keys(JOB_TYPES)

// Type-safe tool validation
function isValidTool(name: string): name is JobType {
  return name in JOB_TYPES
}
```

## Read next

- [REST Jobs API](/docs/api/rest-jobs) — submit and manage jobs
- [SDK Jobs Reference](/docs/api/sdk-jobs) — TypeScript SDK job methods
- [Harness Tools](/docs/api/sessions-tools) — filtered tool discovery for sessions
- [Types & Constants](/docs/api/sdk-types#job_types-registry) — SDK type definitions