eMolecules plug-in for StarDrop
Version This script is for the latest version of StarDrop for either Windows or Mac. To find out which version you have…
3D virtual screening with Surflex eSim3D
When exploring chemistry space around a known hit or lead, you can use 3D virtual screening to identify new compounds…
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
How to be a great drug discovery chemist
Watch our panel of experts as they discuss tactics to achieve success in your medicinal chemistry projects, experiences they’ve had and advice they would give. Learn about the key challenges today’s drug hunter needs to overcome, the skills it takes to gain success across pharma and biotech, and what the future may hold for this industry.
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.
AutoDock Models for the StarDrop Pose Generation Interface (PGI)
From the manuscript “DOCKSTRING: Easy Molecular Docking Yields Better Benchmarks for Ligand Design”, Miguel García-Ortegón, Sergio Bacallado, et al¹ have developed…
R-group clipping of reagents for library enumeration
In this example, using StarDrop’s R-group clipping tool, we will quickly transform chemical building blocks into their corresponding substituents, ready to enumerate a virtual library in StarDrop’s Nova module.
SeeSAR pose – 3D analysis of virtual libraries
This worked example explores ways to assess and design compounds in 3D using the SeeSAR Pose module.
SeeSAR affinity – binding affinity and torsion angle analysis of virtual libraries
This worked example explores ways to assess the binding affinity of docked compounds.
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.
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 releases 3D ligand-based design module for StarDrop drug discovery software
Innovative predictive methods support virtual screening and compound design in the absence of 3D structure data.
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.
Electrostatic-field and surface-shape similarity for virtual screening and pose prediction
We introduce a new method for rapid computation of 3D molecular similarity that combines electrostatic field comparison with comparison of molecular surface-shape and directional hydrogen-bonding preferences (called “eSim”).
