Cross posting from CCL:
Simulated Biomolecular Systems Inc. (SimBioSys) is happy to announce the release of eHiTS 12. eHiTS is a fragment-based molecular docking application that employs a statistically derived scoring function, and includes family-based enhancements for pose generation and scoring.
New improvements and features in eHiTS’ 12 include:
- A new, rigorous protonation state handling mechanism that employs hydrogen bond network optimization and on-the-fly evaluation states. Output structures now include explicit hydrogens.
- A more accurate algorithm for classification of targets to protein-families, considering both geometric and sequence criteria.
- Family-based detection of hot-spots in binding sites, and utilization of those as attraction points during docking.
- Docking constraints can be defined by users by fixing ligand fragments to specified locations, or by requiring specified receptor-ligand interactions to be satisfied.
- A newly trained scoring function using an extended and highly curated knowledgebase of ligand-receptor complexes.
eHiTS’ approach to the docking problem has been unique in various aspects. It divides the ligand to fragments that are docked independently everywhere in the binding pocket, identifies compatible sets of fragment poses that reconstruct full ligand poses, and then optimizes the poses within the binding site. This algorithmic approach guarantees a comprehensive and unbiased sampling of the conformations space. An on-the-fly assessment of protonation states further alleviates potential biases, and reduces the burden on users of structure preparation. The use of protein family knowledge in eHiTS has been shown to improve pose prediction and virtual screening performance. Emphasis is given in eHiTS to ease of use, and optional automated assignment of hydrogens and charges is available.
A major advancement in the technology in the new version is the introduction of target-sites. Prior to docking, local minima are detected by probing the binding pocket thoroughly. Those local minima, along with optional user constraints and automated constraints are used as target-sites – hot-spots that are targeted during pose generation and are promoted by scoring. The use of target-sites gives rise to greater accuracy, and reduced dependence on initial conditions.
Evaluation copies of eHiTS 12 can be obtained by submitting a demo request on our website:
SimBioSys Inc. is a Toronto based company dedicated to development of scientific tools for drug discovery and organic synthesis planning. It retains a constant focus on the innovation of algorithms to provide improved throughput and accuracy in the fields of flexible docking and virtual screening. SimBioSys is also a pioneer in the field of computer-aided retrosynthetic analysis where it supports chemists through the challenges of organic synthesis. With attention to detail, ease-of-use and improved productivity, SimBioSys has built a strong reputation of delivering state-of-the-art scientific solutions to biotechnology, pharmaceutical and other companies in the chemical industry.
For additional information please contact: Orr Ravitz, PhD Chief Operating Officer (416) 741-4263 ravitz (_) simbiosys.com