ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs
We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules.
Extrapolative prediction using physically-based QSAR
Surflex-QMOD integrates chemical structure and activity data to produce physically-realistic models for binding affinity prediction.
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex™-Dock
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.
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.
A structure-guided approach for protein pocket modeling and affinity prediction
We present a hybrid structure-guided strategy that combines molecular similarity, docking, and multiple-instance learning such that information from protein structures can be used to inform models of structure–activity relationships.
Protein function annotation by local binding site surface similarity
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.
Iterative refinement of a binding pocket model: active computational steering of lead optimisation
Computational approaches for binding affinity prediction are most frequently demonstrated through cross-validation within a series of molecules or through performance shown on a blinded test set. Here, we show how such a system performs in an iterative, temporal lead optimization exercise. A series of gyrase inhibitors with known synthetic order formed the set of molecules that could be selected for “synthesis.”
Does your model weigh the same as a Duck?
This article discusses logic fallacies in the context of off-target predictive modelling.
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.
Optibrium demonstrates accelerated lead optimisation in complex agrochemical development
Optibrium’s QuanSA 3D-QSAR method uses an active learning approach to successfully and more efficiently identify a mimic of a macrocyclic natural product
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
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…
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…
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…
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.
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…
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…
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…