January 2015 newsletter

Elucidating the bioactive conformation of CCR5 inhibitors This case study shows how FieldTemplater, working from just a few 2D structures of known active CCR5 Chemokine Receptor inhibitors, was able to correctly reproduce the bioactive conformation of the CCR5 receptor inhibitor Maraviroc as derived from the 4MBS PDB crstal structure, without making use of the X-ray…

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Conformation hunting performance in V10.3

Most of Cresset’s applications require good conformations for molecules in order to produce excellent results. This could be for pharmacophore elucidation (in FieldTemplater module of Forge), virtual screening (in Blaze), searching databases of fragments for new bioisosteres (in Spark) or relating known or newly designed molecules in Forge and Torch. Wherever we need them, we…

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Conformation myths

One of the most common questions we get asked at Cresset relates to our handling of conformations. Our alignment technique uses rigid-body rotations, so we rely on computing conformer populations for molecules whose bioactive conformation is unknown. The generation of useful conformers of flexible molecules is old science: programs have been around since the 1970s…

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Web clip: Using the Cresset Engine Broker to accelerate pharmacophore generation in Forge

The Cresset Engine Broker (CEB) is used to accelerate computationally intensive calculations by connecting resources from a Linux cluster to desktop applications. It is available from both Forge and Spark and can dramatically alter the time needed to complete a large experiment. In this web clip we demonstrate how to use the CEB to accelerate…

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Elucidating the bioactive conformation of CCR5 Chemokine Receptor inhibitors

There are still many projects which do not have a relevant protein-ligand crystal structure to drive compound design. This includes those targeting GPCRs and Ion Channels as well as those working with phenotypic or whole-organism screens. In such cases, field pharmacophore modeling as implemented in FieldTemplater can help to decipher how and which active compounds…

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