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SZYBKI v1.7.0 released

Wed, 02/01/2012 - 01:32 — Anonymous
OpenEye is pleased to announce that SZYBKI v1.7.0 has been released. This is a major new release with numerous new features including an extension to the MMFF94 force field for three coordinated boron compounds.

SZYBKI is available for download now. If a new license is needed, please contact your account manager or business@eyesopen.com to request a new one.

RESOURCES

NEW FEATURES
  • An extension of the MMFF94 force field for three coordinated boron compounds is offered in this release. Most compounds containing B-X bonds where X = C,N,O,S, and H are covered with the following exceptions: X = N(imine), N(sulfonamide), N(pyridinium) and N(quaternary). Also not supported are compounds in which boron is bonded to X=F,Cl,Br,I,B and Si, or makes a bond angle BYX. Compounds in which boron is part of a four-membered ring of B1CCC1 type are also not available in the current parameterization because their existence is questionable: Ab initio calculations at the MP2/6-31G** level failed to identify stable structures for them (highly polar structures in which boron is four-coordinated are formed).
  • A new input flag -solv_dielectric has been added. It controls solvent dielectric for all PB and Sheffield calculations. The default value is 80. The flag -prot_dielectric is changed to -inner_dielectric. The previous flag -prot_dielectric can still be used.
  • A new option flag -salt x that sets the salt concentration for PB calculations has been added. x is the concentration in mM. The default value is 0.
  • A new option -flex_file that allows one to specify only those atoms to be optimized has been added.
  • Starting from the current release, binding entropy (T∆S), can be calculated in a single run:

      szybki -entropy QN -complex pl_complex.oeb -ligands ligands.oeb

    where pl_complex.oeb is a protein-ligand complex file, and ligands.oeb contains an ensemble of ligand conformations in solution.

  • Entropy calculation of protein-bound ligands has been modified. Specifically, the fraction f of ligand surface exposed to the solvent used in the entropy component term: f∆Ss, is calculated currently as f = ALexp/AL, where ALexp and AL are ligand solvent accessible surfaces in the protein complex and solution respectively. The reason for a change is the recent OpenEye internal study which show that the above fraction f calculated according to the equation: f = 0.5(AL - AP + AP L )/AL ([Wlodek-2010]) is for many protein-ligand complexes overestimated.
  • The default value of microscopic surface tension used for protein entropy desolvation calculation is now 6 cal/(molA2) (previously the default value was set at 5 cal/(molA2)). The flag -sfp x, where x is the microscopic surface tension for protein desolvation entropy calculation, allows overriding the default value.
  • Two more flags have been introduced: -t x and -rws. The former sets the temperature x in C for entropy calculations (the default value is 25C). The latter removes water molecules from all solvent accessible surface calculations used for the evaluation of protein-bound ligand entropy, in the case where the input protein contains water molecules.
  • More entropy terms are now reported in the log file. In earlier SZYBKI versions only the total entropy was reported. Starting from 1.7.0 release, in addition to total entropy, configurational, solvation (or partial solvation) and protein desolvation entropy terms are reported.
  • The flag -mol2charges is replaced with -current_charges. -mol2charges is now an alias to the new flag.
  • The format of the log file has been changed to significantly improve its readability.
  • A new option -out_complex has been added. It enables the output of a protein-ligand complex after ligand optimization in partially flexible protein.
BUG FIXES
  • Optimization of polar hydrogens with the -polarH option when the input protein was in the PDB format resulted occasionally in mangling PDB atom names in the protein output file. This bug has been fixed.
  • Combination of flags -complex, -protein_elec PB and -exact_vdw caused a crash on Windows platform. This bug has been fixed.
  • Previous SZYBKI versions produced the parameter and status files even when SZYBKI was run without any user options. This problem has been fixed in the current release.
  • Optimization of ligands in the partially flexible protein receptors in the case when the input file contained more than one ligand, stopped after processing the first ligand. This bug has been fixed.
  • Information on the selected user options was written to the stdout which was making piping impossible. This behavior has been eliminated in the current release.
  • Input molecular files with badly specified geometry (with atom clashes), were not handled properly. Starting from the current release such an input is caught and the processing of such a molecule is skipped.
  • Optimization of large molecules (e.g. optimization of hydrogen positions in very large proteins) can lead to memory exhaustion on some platforms, due to too large amount of VdW interactions or inability to allocate Hessian matrix in the quasi-Newton optimization. Previous SZYBKI releases terminated on such cases with the bad_alloc crash. This has been corrected by terminating the run and generating information on the mentioned above cases, so the user might decrease the number of VdW interactions or switch to conjugate gradient optimization method.
REFERENCES

About OpenEye Scientific Software

OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg, France and Tokyo, Japan. 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:

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, supports 64-bit processing, and runs on Linux, Windows and Mac OS X. For further information on the company and its products, see www.eyesopen.com

For additional information
Joseph Corkery, M.D.
Vice President, Business Development
+1-505-473-7385 x76
Email: business@eyesopen.com