MCP Server

Connect directly to the Pending AI platform from any AI Agent

Model Context Protocol

Pending AI offers a Model Context Protocol (MCP) server for accessing the different tool options. An MCP server gives existing LLM chats a way to call services enabled for a user and streamline different workflows. There are many possible workflow integrations, for example:

Generate a batch of molecules and find any with an amine functional group.

Prompt

Generate some random molecules and find any with an amine functional group.

Response (GPT-4.1)

Here are the generated SMILES that contain an amine functional group (looked for "N", "NH", "NH2" patterns):

1. CCN(CCNCc1cnn(C)c1)C(=O)c1ccccc1N+[O-]
    - Contains secondary and primary amines.
2. C=CCNC(=O)c1cc(-c2ccc(OC)cc2)nc2c(N)c(C(N)=O)oc12
    - Contains primary amine (N), and possibly amidine/amide.
3. NC(c1cc(Br)cs1)c1ccc(Br)cc1OC(F)F
    - Contains primary amine (NC).
4. NS(=O)(=O)c1ccc2c(ccn2C2CCCN(Cc3ccc(Cl)cc3Cl)C2=O)c1
    - Contains sulfonamide (NS(=O)(=O)) and tertiary amine in the ring.
5. Cn1cnc2sc(C(=O)Nc3ccc(N)cc3)cc2c1=N
    - Contains amide (Nc3ccc(N)cc3), and aromatic amine.

These 5 SMILES from the generated set contain at least one amine functional group. Let me know if you want to analyze further or need chemical names.

Perform retrosynthesis on the previously generated molecules.

Prompt

Perform retrosynthesis on the previously generated molecules.

Response (GPT-4.1)

Retrosynthesis jobs have been submitted for the 3 generated molecules:

CC(O)C(C)Nc1nc2ncnc(SCc3ccccc3F)c2s1 — Job ID: 691e6e6f53b31257cbcbd91c
CCOC(=O)CN1C(=O)C(=Cc2ccc(N(CC)CC)cc2)C=C(CC)C1=O — Job ID: 691e6e7044369a3ca4510ae4
CC1CCCC(Nc2cc(C(F)(F)F)nc(CC3CC3)n2)CC1 — Job ID: 691e6e70f7acb63a247fa8f8
Each job is currently in "submitted" status. Let me know if you want to poll for results or retrieve the completed routes when ready.

Poll the retrosynthesis jobs and find the one with the longest route.

Prompt

Poll the retrosynthesis jobs and find the one with the longest route. 

Response (Sonnet 4.5)

Summary
After polling all 27 retrosynthesis jobs, I found the longest synthetic route:

🏆 Winner: 6-Step Synthesis
Target Molecule: CSCCCCCSc1nc2c(c(=O)[nH]1)C(N)CC2
Job ID: 691fed6eaaa8ae1c9767f0dd
Amine Type: Primary amine

The 6-Step Route:
1. Core oxidation - Oxidize tetrahydropyrimidine scaffold
2. Chlorination - Install leaving group at reactive position
3. Reductive amination - Introduce primary amine
4. Bromination - Prepare alkyl bromide linker
5. Thiol formation - Convert bromide to thiol
6. Thioether coupling - Final SNAr to connect linker to core

Key Statistics:
- Total molecules analyzed: 27
- Completed routes: 23
- Route lengths found:
  - 6 steps: 1 molecule (longest)
  - 5 steps: 1 molecule
  - 4 steps: 1 molecule
  - 3 steps: 2 molecules
  - 2 steps: 5 molecules
  - 1 step: 3 molecules

Files Created:
- View longest route analysis
- View detailed 6-step synthesis

This complex heterocyclic molecule with a bis-thiol linker represents the upper end of synthetic accessibility among the randomly generated structures, requiring sophisticated multi-step synthesis with careful functional group manipulation.

As Pending AI continues to deliver new possibilities, when in doubt you can always ask "What am I able to do using Pending AI?" for more information.

Supported Tools

The Pending AI MCP server currently supports the following tools in Early Access:

Tool	Description
list_retrosynthesis_engines	List retrosynthesis engines. Use this tool to show available machine learning architectures and search strategies that can be used when submitting retrosynthesis jobs. Engine choice can impact the quality and diversity of retrosynthetic routes found.
list_retrosynthesis_libraries	List retrosynthesis libraries. Use this tool to show available building block libraries that can be used when submitting retrosynthesis jobs. Libraries specify collections of molecules that are available starting materials for a retrosynthetic search.
list_retrosynthesis_jobs	List retrosynthesis jobs. Use this tool to get short summaries of existing jobs, or to find a job_id based on SMILES and creation timestamps. Pagination is supported via offset-based page and limit parameters.
create_retrosynthesis_job	Create a retrosynthesis job. Use this tool to submit a molecule for retrosynthesis screening and provide optional parameters to customise the search behaviour. The molecule should be provided in SMILES format. A job_id is returned that can be used to poll the job status and retrieve results once it has completed.
retrieve_retrosynthesis_job	Retrieve a retrosynthesis job. Use this tool to fetch the details of a previously created retrosynthesis job by its id. Each job contains the molecule SMILES, status, and added timestamps for simple summary information.
retrieve_retrosynthesis_job_status	Retrieve the status of a retrosynthesis job. Expect a value that changes over time from submitted (waiting to be processed) to processing (actively being processed) to completed or failed (finished processing). Use this tool for polling the status of a job before before results become available.
retrieve_retrosynthesis_job_result	Retrieve the results of a previously submitted retrosynthesis job by its id. The list of retrosynthetic routes that were computed contain the synthetic steps to make the molecule with relevant building blocks. See the documentation for details about how retrosynthetic routes are represented.
delete_retrosynthesis_job	Delete a retrosynthesis job and generated results. The job will no longer be accessible. The operation is irreversible and should be used with caution. You cannot delete a job that is still processing.
list_molecule_generator_models	List generative models for sampling molecules. Use this tool to retrieve models and their metadata that can be used to see if a model is online and ready for sampling.
create_molecule_generator_sample	Sample molecules from a generative model. Molecules are represented in SMILES format and contain drug-like properties unique to the model used. Use this tool to generate novel structures that can be further filtered and evaluated. Conditional filtering should be applied after sampling to select relevant molecules.

Authentication

The MCP server aligns with current OAuth2.0 authentication flows allows for Dynamic Client Registration. Upon connecting to the server from the integrated tool connectors such as Claude or VSCode, you will be prompted to log in with your Pending AI account without any further steps.

If you are connecting from a service that is not one of the supported connectors, contact our team so that we can help provide any required callback URLs for your particular use case. For ease of testing, the MCP server already supports a callback on http://localhost:8000/auth/callback as used by most frameworks.