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…
Enamine screening collection
StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop. Enamine’s commercially available screening…
MolPort screening collection
StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop. MolPort’s commercially available screening…
eMolecules screening collection
StarDrop users who have licensed the Surflex eSim3D module can freely download prepared virtual screening collections for use in StarDrop. eMolecules‘ commercially available screening…
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”).
Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose
We introduce the QuanSA method for inducing physically meaningful field-based models of ligand binding pockets based on structure-activity data alone.
Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes
Here we present an analysis of novel drug/target predictions, focusing on those that were not obvious based on known pharmacological crosstalk.
Chemical Structural Novelty: On-Targets and Off-Targets
To compare chemical structures, we can look at a number of 2D and 3D characteristics. In this paper, a group of 358 drugs with overlapping pharmacology were assessed for chemical similarity, using a new framework.
