LABORATORY INFORMATICS
Confident chemistry
SOPHIA KTORI EXPLORES THE ROLE CHEMINFORMATICS SOFTWARE PROVIDERS PLAY IN SUPPORTING SCIENTISTS IN ACADEMIA AND INDUSTRY TO BETTER UNDERSTAND THE PROPERTIES OF POTENTIAL NEW DRUGS
OpenEye Scientific develops and offers large-scale molecular modelling applications and
toolkits, primarily aimed at drug discovery and design. ‘Although our tools are used by a wider industrial sector, from large pharma and small biotechs, through to agrochemicals and materials scientists,’ commented Ashutosh Jogalekar, associate director – applications science at OpenEye Scientific. OpenEye Scientific was established
some 25 years ago, to build on the founders’ conviction that shape and electrostatics are the two key factors that are responsible for molecular recognition, which, in turn, drives how drugs work, ‘… because most drugs are small molecules that interact with proteins,’ Jogalekar continued. ‘So, being able to accurately model shape and electrostatics was really the foundational principle of the company.’ Cloud computing has been a significant
driver of speed and scale as the need to work with huge numbers of compounds, and volumes of disparate data, has increased, Jogalekar continued. ‘We now have access to almost unlimited processing power, and we can use platforms such as Amazon Web Services (AWS) to recruit hundreds of CPUs and GPUs, if required, to help us search through a billion compounds in just a matter of hours.’ That’s been really transformative, Jogalekar commented. ‘Running our solutions on AWS means we can look at solving modelling queries and investigations that would previously have been impossible due to hardware or compute time limitations.’
A one-stop shop for drug discovery OpenEye Scientific’s flagship solution,
14 Scientific Computing World Autumn 2021 Andrew Leach
Orion, a molecular design platform, is – as far as the company is aware – the only cloud-native, comprehensive molecular modelling and cheminformatics platform, which Jogalekar described as ‘a one-stop shop where scientists can come and do all kinds of cheminformatics and modelling calculations on compounds, including large-scale virtual screening, calculation of physicochemical properties and molecular dynamics’. Orion provides users with an integrated
web-based solution for designing, calculating, viewing and analysis in the chemical space, and offers a dedicated platform for managing data and applications. This single platform negates the need to swap between apps, and also means that data doesn’t have to be transferred from one tool to another,
but can remain in the Orion platform. ‘Orion effectively wraps up all the other
applications that OpenEye Scientific has developed into a single solution, which includes tools for calculating shape and electrostatics,’ Jogalekar continued, ‘along with at least a dozen other applications that can be used to carry out all kinds of other cheminformatics protocols.’ Orion presents a set of workflows, which
OpenEye Scientific has termed ‘floes’. ‘So, one floe will calculate key properties of compounds, such as their solubility for instance, while another can search for compounds that are similar to an existing patented compound of interest. All of these floes are available, essentially at the click of a button. All the user has to do is log in to their account, upload critical inputs and go from there.’
Solving data integration and curation issues and providing the tools that will help to rapidly evolve machine learning and AI tools are, respectively, the main challenges and future-focused goal for the evolution of cheminformatics across fields, he suggested. ‘People are going to want to visualise and analyse not just more data, but more
“We can use platforms such as Amazon Web Services to recruit hundreds of CPUs and GPUs, if required, to help us search through a billion compounds in just a matter of hours”
@scwmagazine |
www.scientific-computing.com
Carrie Tang
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