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Publications & Presentations


Hydrogen Bonding: Ab Initio Accuracy From Fast Interatomic Gaussian Approximation Potentials

Thursday, 23 August 2018 12:26
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Mario Öeren

Mario Öeren gave this presentation at the ACS Fall 2018 National Meeting & Exposition held in Boston, USA.

Abstract

Non-covalent, electrostatic interactions play a significant role in many chemical applications and evaluating their strength is crucial for progress in fields such as drug design and material science. In most cases, due to the nature of these interactions, ab initio calculations are required to accurately assess their strength. However, due to their computational cost, ab initio methods are not suitable for screening datasets with large numbers of structures.

We will present a method based on Gaussian approximation potentials (GAPs), which are interatomic potentials trained on ab initio data using machine learning. While GAPs could be applied to any interaction, we chose hydrogen bonds as an example for this presentation. We will describe the workflow to prepare the GAP training set, how to generate GAPs from density functional theory data using the software QUIP and how to calculate the hydrogen bond energies for a structure from the resulting model. Such an approach allows us to achieve results close to ab initio accuracy, but with significantly lower computational costs. The results are validated against the ab initio calculations and quantum theory of atoms in molecules results.

While GAPs have been mostly used for molecular dynamics simulations of bulk crystals, they can be applied to a variety of problems which require the exploration of a complex potential energy surface (PES); for example, the hydrogen bond energy model described herein can be used in scoring functions for protein-ligand interactions.

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Preprint: WhichP450

Tuesday, 13 February 2018 16:26
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Peter Hunt

This paper appears in J. Comput.-Aided Mol. Des. and describes the underlying methods and validation of the new model predicting the most likely Cytochrome P450 isoforms responsible for metabolism of a compound in StarDrop's P450 module.

WhichP450 and regioselectivity prediction

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Latest Forums


Re:Decimal places in an export?

Friday, 03 August 2018 03:44

Thanks for your question Andre. Unfortunately, as you have noted, the number of significant figures in exported values is fixed at the moment. We've noted the problem and will address this a soon as possible in a future version. Sorry for the inconvenience and thanks again for pointing this out.


Category: General - How Do I...?
Views: 0

Decimal places in an export?

Tuesday, 31 July 2018 07:42

Hi there, I have set the decimal places in the molecular weight column to 2 and they are displayed as two. However, when I export to csv or text, or when I copy and paste into Excel, I only get 1 decimal place in my export. Is there a way to change that? Thank you very much in advance. Best regards Andre


Category: General - How Do I...?
Views: 2217

We're Hiring: Marketing and Software Engineers

Tuesday, 31 July 2018 01:57

As part of our exciting plans for future product enhancement and growth we are looking to recruit two C++ software engineers to work on client- and server-side code development of Optibrium's cheminformatics and computational chemistry software product range. In addition, we are looking to recruit a Marketing Associate responsible for planning, developing and implementing the company’s marketing...


Category: Optibrium News & Announcements
Views: 1367

Popular Downloads


Enamine Plug-in for StarDrop

Friday, 31 August 2018 09:06

This script enables you to search the EnamineStore, a database of their commercially available screening compounds and chemical building blocks. This will return details about the availabilitty of specific compounds and find those that are structurally similar to your most interesting hits and leads or contain relevant substructures.

The installer file and instructions for how to install and use the script are provided in the following pages...

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