Calculate on the cloud

Posted by
Ákos Tarcsay
on 03 10 2022

Enriching chemical structures with chemical domain information by calculated properties contributes to rationalizing workflows in chemistry. In order to increase the flexibility, access and integrability, Calculators and Predictors have been made available as a REST API SaaS via AWS Marketplace to offer a wide range of high-quality chemical descriptors including phys-chem properties, tautomerization and structural descriptors seamlessly.

As a result of more than 20 years of continuous development Chemaxon provides world-class calculated properties. According to the independent, blind SAMPL benchmark challenge data, Chemaxon protonation (pKa) and partitioning (logP, logD) predictions are providing outstanding accuracy.

Simple access is provided through automatic subscription, free of charge (Figure 1). The calculators are available as a pay per use service that ensures full flexibility in selecting from the provided endpoints and executing different amounts of calculations.Figure 1. Subscription workflow.

The system was designed to execute calculations in a robust and secure way with low latency (Figure 2). Autoscaling of the Elastic Container Service and multi-regional deployment ensures prompt response time. Chemaxon software development processes are conform to the Information Security Management System standard: ISO/IEC 27001:2013 to ensure that code quality and software security aspects are integrated into the whole development pipeline. AWS customers are offered to call the services through PrivateLink technology to communicate via the AWS backbone network, without passing the public internet. The stateless service was built in a way that the processed structures are not stored in any form. Learn more about the details in the AWS product specific documentation and take a look at the curl, Python, JS and Java code snippets to get started without hassle.

Figure 2. System overview.

Scalability has been tested with 8.8 Mcule ( by posting 25 structure batches in 50 parallel threads to calculate CNS-MPO score. The results revealed a median of 53 ms/cpd per thread, that translates to ~1 ms /cpd sustained performance. In case of  CNS-MPO calculation pKa, logP, logD, HBDA, MW and PSA values are returned along with the CNS-MPO score, this translates to 167 µsec per calculation cycle per molecule. 

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