Szybki TK 1.8.4

New features

• A new OESingleConfResult::GetRelLnQ method has been added for retrieving the logarithm of the relative vibrational-rotational partition function with respect to the minimum free-energy conformation.

Major bug fixes

• Previously, when protein-ligand systems where ligands were made of two or more molecules (for example, an inhibitor + water molecule), interligand IEFF interaction energy was not correctly calculated in two cases: (1) for single point calculations and (2) for solid-body ligand pose optimization. In both cases, the total protein-ligand interaction energy was not affected. In the second case, optimization itself was not affected. This issue has been fixed.

Minor bug fixes

• Internal refactoring has been performed to improve stability.

• Memory leaks related to protein-ligand interaction and handling protein flexibility have been fixed.

API Changes

• The unused OEMMFFSubsetVdw class has been removed.

Documentation fixes

• Cross-references have been fixed in several sections.

Java- and C#-specific changes

• The following examples were added for Java and C#:

  • Ligand in vacuum optimization

  • Optimize multiple ligands in Sheffield solvation model

  • Partially flexible protein optimization

  • Partially flexible protein with Newton-Raphson optimization

  • FreeForm Solvation

  • FreeForm Conformer

  • Entropy of a bound ligand

  • Bound ligand optimization

  • Rigid receptor optimization

  • Newton-Raphson optimization

  • Bound and solution entropy

  • PB Protein-ligand binding