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…
What are conformational ensembles? A conformational ensemble is a collection of the different 3D shapes a molecule can adopt in…
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…
CAMBRIDGE, UK, 22 October 2024 – Optibrium, a leading developer of software and AI solutions for molecular design today announced…
Introduction Using the integrated set of computational methods within the BioPharmics™ Platform, macrocycles can be effectively modelled for lead optimisation.…
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.
We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on ligands whose bounds structures were determined later. The knowledge-guided docking protocol was tested on a set of ten protein targets using a total of 949 ligands.
Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk.
This paper demonstrates how the Surflex-PSIM method can help investigate hypotheses around protein function in cases where function cannot be determined by sequence similarity.
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.
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.
To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures.
In this paper, we describe an extended benchmark for non-cognate docking of macrocyclic ligands, and the superior performance of Surflex-Dock…