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…
Binding affinity prediction continues to be a challenge in computer-aided drug design, especially in the absence of a high-quality target…
In our recent article in Innovations in Pharmaceutical Technology, we explore the principles, techniques, and applications of structure-based and ligand-based…
Introduction Using the integrated set of computational methods within the BioPharmics™ Platform, macrocycles can be effectively modelled for lead optimisation.…
Introduction 3D molecular modelling plays a vital role in modern drug discovery, offering powerful applications to streamline research, reduce costs,…
New PyMOL interface extends access to Optibrium’s structure-based design method Surflex-Dock CAMBRIDGE, UK, 04 February 2025 – Optibrium, a leading…
What comprises large molecules? When we talk about “large molecules,” we often think of biologics like monoclonal antibodies, proteins, and…
Buying software for your company can be a challenge. Every organisation does things differently, and there is often no handbook…
CAMBRIDGE, UK, 22 October 2024 – Optibrium, a leading developer of software and AI solutions for molecular design today announced…
In this paper, we describe an extended benchmark for non-cognate docking of macrocyclic ligands, and the superior performance of 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.
Macrocycles are becoming increasingly popular in drug discovery, due to their vast potential against previously “undruggable” targets. But the size…
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.
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.
BioPharmics’ Drs Ajay Jain (CEO) and Ann Cleves (Director of Applied Science) join the Optibrium team as Vice Presidents in the newly-created BioPharmics Division
Systematic optimisation of large macrocyclic peptide ligands is a serious challenge. Here, we describe an approach for lead optimisation using the PD-1/PD-L1 system as a retrospective example of moving from initial lead compound to clinical candidate.
The solution structure of the minor conformer of rapamycin was investigated using a combination of NMR techniques and computational methods
We show that the distribution of expected global strain energy values is dependent on molecular size in a superlinear manner. The distribution of strain energy follows a rectified normal distribution whose mean and variance are related to conformational complexity.
We present results on the extent to which physics-based simulation (exemplified by FEP+) and focused machine learning (exemplified by QuanSA) are complementary for ligand affinity prediction.
In this webinar, we demonstrate intuitive workflows for 3D ligand-based drug design