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…
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.
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.
Optibrium acquires BioPharmics LLC, expanding its 3D drug design and visualisation offering
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
Complex peptide macrocycle optimisation: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
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.
Unmasking the true identity of rapamycin’s minor conformer
The solution structure of the minor conformer of rapamycin was investigated using a combination of NMR techniques and computational methods
A distributional model of bound ligand conformational strain: from small molecules to large peptidic macrocycles
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.
Synergy and complementarity between focused machine learning and physics-based simulation in affinity prediction
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.
3D ligand-based drug design: webinar
In this webinar, we demonstrate intuitive workflows for 3D ligand-based drug design
eSim3D: electrostatic-field and surface-shape similarity for ligand-based drug design
In this webinar, we present eSim3D, a novel ligand-based drug design approach based on electrostatic-field and surface-shape similarity coupled with unique conformational search capabilities, offering unprecedented accuracy and performance.
Conformational strain of macrocyclic peptides in ligand–receptor complexes based on advanced refinement of bound-state conformers
To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures.
XGen: real-space fitting of complex ligand conformational ensembles to x-ray electron density maps
We report a new method for X-ray density ligand fitting and refinement that is suitable for a wide variety of small-molecule ligands, including macrocycles.
Structure- and ligand-based virtual screening on DUD-E+: performance dependence on approximations to the binding pocket
Using the DUD-E+ benchmark, we explore the impact of using a single protein pocket or ligand for virtual screening compared with using ensembles of alternative pockets, ligands, and sets thereof.
