Why does conformational flexibility matter in drug design?
What are conformational ensembles? A conformational ensemble is a collection of the different 3D shapes a molecule can adopt in…
How much does 3D molecular modelling software cost?
Introduction 3D molecular modelling plays a vital role in modern drug discovery, offering powerful applications to streamline research, reduce costs,…
Optibrium Widens Access to Industry-Leading Docking Method
New PyMOL interface extends access to Optibrium’s structure-based design method Surflex-Dock CAMBRIDGE, UK, 04 February 2025 – Optibrium, a leading…
How can I run a successful virtual screen?
Virtual screening is often powerful because it is fast (i.e., cheap) and can give new insights into your project much…
How can I model large molecules like macrocycles?
What comprises large molecules? When we talk about “large molecules,” we often think of biologics like monoclonal antibodies, proteins, and…
Optibrium demonstrates superior molecular docking method for small molecules and macrocycles
CAMBRIDGE, UK, 22 October 2024 – Optibrium, a leading developer of software and AI solutions for molecular design today announced…
Ligand-based drug design using Surflex eSim 3D
This worked example uses StarDrop’s Surflex eSim3D module to assess a small library of compounds for their similarity to known Heat Shock Protein 90 (HSP90) ligands.
MPO explorer: sensitivity analysis
In this example, we will use the Sensitivity Analysis tool in StarDrop’s MPO Explorer module to check if the ranking of compounds in a data set is sensitive to any of the criteria or importance values in a scoring profile.
MPO explorer: automatically building a scoring profile with rule induction
In this example we will use the Profile Builder in StarDrop’s MPO Explorer module to derive a multi-parameter scoring profile, based on a CNS data set.
Guided multi-parameter optimisation of 2D and 3D SAR
This SeeSAR and ADME QSAR worked example uses a combination of 2D and 3D methods to understand and optimise a virtual library of Heat Shock Protein 90 (HSP90) inhibitors.
Physical model induction with QuanSA™: Affinity prediction that is synergistic with simulation-based methods
The QuanSA method To define a ‘pocket field’, an initial alignment of all training molecules is constructed and function parameters…
How to perform fast and accurate 3D ligand-based affinity predictions
Binding affinity prediction continues to be a challenge in computer-aided drug design, especially in the absence of a high-quality target…
Macrocyclic peptide optimisation: Integrating computational approaches with biophysical data
Introduction Using the integrated set of computational methods within the BioPharmics™ Platform, macrocycles can be effectively modelled for lead optimisation.…
Molecular docking: Extrapolating to new scaffolds with Surflex-Dock
Interested in improving your binding mode predictions? Surflex-Dock is a unique method for molecular docking, offering automatic pipelines for ensemble docking, applicable to both small molecules and large peptidic macrocycles alike.
Macrocyclic lead optimisation
Macrocycles are becoming increasingly popular in drug discovery, due to their vast potential against previously “undruggable” targets. But the size…
Challenges and approaches in 3D ligand-based drug design
Ann and Ajay discuss the science behind and applications of the eSim molecular similarity method, a ligand-based drug design approach which considers surface-shape, electrostatics, and directionally sensitive hydrogen-bonding when comparing two molecules.
Imputation of sensory properties using deep learning: webinar
In this webinar, we demonstrate how Augmented Chemistry®, a unique deep learning method, can learn from higher throughput data together with limited panel data to provide high-quality imputations for sensory properties.
Optibrium demonstrates accelerated lead optimisation in complex agrochemical development
Optibrium’s QuanSA 3D-QSAR method uses an active learning approach to successfully and more efficiently identify a mimic of a macrocyclic natural product
Chemical Structural Novelty: On-Targets and Off-Targets
To compare chemical structures, we can look at a number of 2D and 3D characteristics. In this paper, a group of 358 drugs with overlapping pharmacology were assessed for chemical similarity, using a new framework.
