Release Highlights 2020.2.2¶
The OEApplications 2020.2.2 is a bug-fix of the OEApplications 2020.1 release, and depends on OEToolkits 2020.2.2. Click on the below links for more information about the bug fixes in this release:
Release Highlights 2020.2¶
OMEGA: New fragment library¶
A new enhanced fragment library has been created for use in OMEGA. The new fragment library consists of more than 500,000 fragments that have been generated using the MMFF force field.
This library is designed to reduce the run time of large-scale conformer
and therefore is not built into OMEGA but is available as a separate download.
To run OMEGA with the enhanced library, simply use the command line flag
The fragments have been collated from commonly used electronic databases, such as Enamine Building Blocks. Consequently, dramatic runtime performance improvements can be seen for the Enamine Real dataset, among others, since less time is spent building fragments on the fly. Runtime performance improvements can be seen for all datasets; the Platinum and Enamine Real sets show particular improvement and run ~50% faster (benchmarks run on Ubuntu 16 with Intel(R) Xeon(R) Gold 6128 CPU 3.40GHz and NVIDIA Tesla V100 GPU).
The enhanced fragment library generates the same high-quality conformers as the built-in library, as shown by the minimum RMSDs of the filtered Platinum dataset.
We are eager to get your feedback on the new enhanced fragment library. Please share your experience with us at firstname.lastname@example.org.
OEDOCKING: Improved receptors¶
Receptors used in the OEDocking TK and the OEDOCKING applications,
including FRED, HYBRID and POSIT, have been improved
to take advantage of properly prepared structures from SPRUCE. A new
OEReceptor object has been introduced and is created and contained within an
OEDesignUnit. Since an
OEReceptor is now an integral part of an
OEDesignUnit, it is saved into an
OEDU file along with a design unit.
There is no separate I/O for the receptors.
Having the receptors as part of the design unit with properly prepped structures
makes it easier for the docked and posed structures to be used in further downstream
modeling, which is especially necessary with protein force fields like
new receptor also assists with more flexible use of modern force fields like
Parsley in POSIT.
SZYBKI: A new protein force field¶
AMBER FF14SB protein force field has been implemented in OEFF TK. This
new force field has also been made available in SZYBKI for optimizing both
protein and protein-ligand complexes.
FF14SB is the most widely used protein force field for molecular dynamics or
any other force field-based calculations. It is also used in Orion molecular dynamics
package, and is the community gold standard for such calculations.
10.13, 10.14, 10.15
Support for Ubuntu16 has been dropped. Support for Ubuntu20 has been added.