We are delighted to announce that the OPSIN web app has become a member of the Chemical Biology Services here at EMBL-EBI and can be accessed at: https://www.ebi.ac.uk/opsin OPSIN converts systematic IUPAC names to structures, and is an invaluable service for curators of chemical and biochemical structures or automated chemical text-mining systems. It was originally developed at the University of Cambridge by the Peter Murray-Rust group, with Daniel Lowe continuing to develop it since then. Here's a quote from the History page on the original website: During the development of OSCAR the need to have a program to convert identified chemical names to connection tables arose. Due to the absence of any open source efforts with broad coverage of organic nomenclature work was started by Peter Murray-Rust and Joe Townsend on such a program. This work was continued by Peter Corbett culminating in the creation of a system broadly similar to the current incarnation ( Corbett and...
Dear SureChEMBL users, Welcome to the third blog post in our SureChEMBL2.0 series! If you missed the previous ones [ 1 , 2 ], be sure to check them out when you have a moment. Today, we're diving into what has changed under the hood of SureChEMBL! At the end of last year, we announced the integration of RDKit for compound depiction and various types of chemistry searches. But of course, we didn’t stop there. In line with our goal to simplify the service architecture, but also to improve the data quality, we’ve decided to follow the lead of our sister resource ChEMBL in how we manage compound structures. What’s Changing? SureChEMBL handles compound structures at several stages in the pipeline. Regardless of how a compound is identified in a patent, the first step is to standardise its structure — and we’re now using the ChEMBL standardiser for this. Next, we register compounds using an RDKit-based hash , which helps us avoid introducing duplica...