HazELNut

Version 2.0 [201509]

Export, Normalize and Exploit Reactions from ELNs

Synthetic chemistry is at the core of pharmaceutical drug discovery. Although small molecule informatics is well understood and supported by multiple vendors, the field of reaction informatics is relatively under-developed. Unlike molecular modelers and computational chemists, real bench chemists have relatively few software tools to assist them in the process of making molecules (efficiently, the first time, and in sufficient yield). A better understanding of chemical reactions can be used to improve the design-make-test cycle, both for in-house synthesis and outsourcing to contract research organizations (CROs).

NextMove Software's HazELNut suite of tools is designed to help pharmaceutical companies unlock and exploit the wealth of knowledge in their own in-house Electronic Lab Notebook (ELN) systems. The raison d'etre of most ELNs is to capture intellectual property, such as assisting in patent filings, with data analysis and exploitation often overlooked or afterthought. As a result, these systems are optimized from fail-safe transactions, audit logs and fine-grain security, making even simple queries and analysis difficult, slow or impossible.

Whilst initially designed to assist in the export of reaction databases as reaction SMILES, MDL RXN or MDL RD files (containing experimental data such as reactant volumes, temperature, product yields and experimental write-ups) from Perkin Elmer Informatics' (formerly CambridgeSoft's) e-Notebook ELN and BioVia's (formerly Accelrys/Symyx) ELN systems, the HazELNut suite has evolved to also encompass downstream reaction processing independent of the data source; operations such as reaction normalization, duplicate checking/elimination, atom-mapping analysis, role assignment, 2D co-ordinate generation, reaction similarity searching and so on.

As of mid of 2015, HazELNut has sucessfully been used at eight out of the top twelve pharmaceutical companies.

CaffeineFix is used to rapidly match chemical names or terms against a dictionary or grammar (e.g. a grammar for IUPAC names). As well as use in text-mining, it can be used to provide autocomplete functionality and spell-correction.

Casandra is a server for delivering real time safety warnings of experimental hazards straight to the pharmaceutical electronic laboratory notebooks (ELNs).

HazELNut is a suite of tools used to extract, normalize and analyse information in Electronic Lab Notebooks (ELNs). This can be used to implement a search interface, find/eliminate duplicates, find similar reactions and so on.

LeadMine extracts chemical names and terms from text. It incorporates NextMove's CaffeineFix technology to find terms that match appropriate dictionaries or grammars. It has enhanced functionality to handle the patent literature.

Matsy is a set of tools for creating and analysing Matched Molecular Series (the general form of Matched Molecular Pairs). In particular, it can be used to suggest what compound to make next in a Medicinal Chemistry program.

MPSearch rapidly searches a database to find Matched Pairs related to a query molecule. This type of search is used to explore previous medicinal chemistry strategies.

NameRXN is used to classify and name reactions. It is particular useful in the context of ELN analysis but also as a plugin to chemical drawing software. NameRXN builds on NextMove Software's Patsy technology.

Patsy is used to speed up SMARTS pattern matching by creating optimized SMARTS patterns or source code. Speed gains are particularly large when multiple SMARTS patterns are matched against a single structure.

SmallWorld is an index of chemical space based on more than 4 billion molecular substructures. It can be used to measure similarity based on graph-edit distance, find the MCS of two or more molecules, analyse HTS results and much more.

Sugar & Splice can be used to perceive and depict biopolymer structure. It makes it easy to interconvert between small-molecule representations (e.g. SMILES, MOL) and biopolymer representations (HELM, IUPAC line notation).