How can I predict binding affinity without a target protein structure?
Why traditional ligand-based QSAR methods have fallen short You might be sceptical about ligand-based QSAR approaches; many researchers are. We discussed why there has…
Ensemble-based conformational modelling for macrocycles
From X-ray refinement to lead optimisation Conventional ligand-fitting and refinement methods in X-ray electron density maps often yield models with…
xGen™: Fitting of complex ligand conformational ensembles to X-ray electron density maps
Conventional ligand fitting and refinement in X-ray electron density maps relies on single conformers and B-factors, that often yields ligands…
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…
Leveraging structure-based and ligand-based techniques in drug discovery
In our recent article in Innovations in Pharmaceutical Technology, we explore the principles, techniques, and applications of structure-based and ligand-based…
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 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…
How do I get budget approval for drug discovery software?
Buying software for your company can be a challenge. Every organisation does things differently, and there is often no handbook…
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…
Physical Parameter Estimation vs. Pure Machine-Learning for Drug Design
Nearly all computational methods in the CADD field depend on parameters whose values are derived from various types of experimental…
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.…
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands
In this paper, we describe an extended benchmark for non-cognate docking of macrocyclic ligands, and the superior performance of Surflex-Dock…
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…
From UK-2A to florylpicoxamid: active learning to identify a mimic of a macrocyclic natural product
Scaffold replacement as part of an optimisation process that requires maintenance of potency, desirable biodistribution, metabolic stability, and considerations of synthesis at very large scale is a complex challenge.
