Freeform –calc conf
Freeform –calc conf estimates the free energy of transforming a single molecular conformer from an ensemble of solution phase conformers to a single bioactive conformation. Several new features have been added, including:
- Multiple input conformers can now be tracked. For example, input conformers could be top scoring poses of docked molecules, alternative x-ray conformations (from the PDB), or alternative ligand refinements (e.g. from AFITT).
- In addition to the standard Sheffield solvation model, Freeform energy calculations can now be run using a Poisson-Boltzmann corrected solvation model.
- Conformational search has been improved by including solvation throughout the conformational sampling.
- An extension of the AM1BCC charging model that considers Electrostatically Least-interacting Functional groups (ELF), AM1BCC ELF10, is now the default method for applying partial charges to a ligand. This mitigates electrostatics problems that frequently arise for charged ligands.
Multiple input conformers can now be tracked. Above, the top 9 docked poses of a renin inhibitor (red circles) are evaluated for their ligand strain relative to the entire unbound aqueous ensemble (blue triangles).
The SZYBKI app has been streamlined. Changes include:
- SZYBKI command-line options have been reorganized into simpler groups.
- Torsions can now be constrained by providing four atomic indices that define them when minimizing ligands.
- User-selected residues are now allowed to move during the optimization of protein-bound ligands.
- Support for Ubuntu 14 has been added.
- Support for RedHat 7 has been added.
- Support for Mac OS X 10.10 and 10.11 has been added.
- Mac OS X 10.7 and 10.8 are no longer supported.
- SuSe 11 is no longer supported.
SZYBKI is now available for download. Existing licenses will continue to work, but if a new license is required, contact your account manager or email firstname.lastname@example.org.
About OpenEye Scientific Software
OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, NM, with offices in Boston, Cologne, Strasbourg, and Tokyo. It was founded in 1997 to develop large-scale molecular modeling applications and toolkits. Primarily aimed towards drug discovery and design, areas of application include:
- Structure Generation
- Shape Comparison
- Fragment Replacement
The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors and runs on Linux, Windows and Mac OS X.
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