SimBioSys (short for Simulated Biomolecular Systems) is a Toronto-based chemistry software company focusing on structure based drug discovery and retrosynthetic analysis tools. It has established a strong reputation as one of the leading developers of flexible docking applications, virtual screening methods and computer aided organic synthesis design.
|Headquarters||Toronto, ON, Canada, |
|Zsolt Zsoldos, Chief Technology Officer|
|Parent||John Wiley & Sons|
In 2014, SimBioSys was acquired by John Wiley & Sons as part of their Research division.
Areas of Expertise
Founded by a group of computer scientists and chemists, SimBioSys combines sophisticated search algorithms, machine learning techniques and informatics approaches with chemical knowledge and modelling.
- eHiTS - A fragment based flexible docking software. eHiTS uses an exhaustive and systematic search algorithm that is designed to find the global minimum energy pose of ligands in proteins' binding pockets. The application uses SimBioSys' proprietary scoring function. In 2008 the company ported its docking software to Sony's PlayStation 3 and other Cell Broadband Engine platforms to achieve higher screening speeds. That created huge interest especially with researchers using PlayStation 3 cluster technology.
- LASSO - A similarity based virtual screening tool that uses elements of eHiTS scoring function to identify bioactive molecules in large libraries of compounds.
- ARChem - A retrosynthetic analysis tool that searches for possible synthetic routes from commercially available starting materials to target molecules.
- CheVi - SimBioSys' 3D molecular visualization software.
ARChem and CIRX (Fiz Chemie) were combined to create Wiley ChemPlanner, which is now exclusively licensed by Wiley Science Solutions to Chemical Abstracts Service.
SimBioSys maintained a marketing partnership with KeyModule, distributing the UK based company's lead design tool, SPROUT, as well as other products.
- Collins, Allison. "John Wiley Continues Deal Spree, Buys SimBioSys". Mergers & Acquisitions, Latest News. Retrieved 2014-09-06.
- Zsoldos, Zsolt; et al. (July 2007). "eHiTS: A new fast, exhaustive flexible ligand docking system". Journal of Molecular Graphics and Modelling. 26 (1): 198–212. doi:10.1016/j.jmgm.2006.06.002. PMID 16860582.
- Englebienne, Pablo; Moitessier, Nicolas (June 2009). "Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins?". Journal of Chemical Information and Modeling. 49: 1568–1580. doi:10.1021/ci8004308. PMID 19445499.
- Reid, Darryl; et al. "LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening". Journal of Computer-Aided Molecular Design. 22: 479–487. doi:10.1007/s10822-007-9164-5.
- James. "Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation". Journal of Chemical Information and Modeling. 49: 593–602. doi:10.1021/ci800228y.
- Results of Merck's comparative enrichment study for molecular docking software at Archive.today (archived 2013-01-15)
- SimBioSys official site at the Library of Congress Web Archives (archived 2002-09-15)
- SimBioSys-Blog official blog site at Archive.today (archived 2013-01-15)
- ARChem Route Designer presentation presentation on ARChem by Antony Williams
- Free Virtual Screening Service on ChemSpider; LASSO virtual screening was integrated with ChemSpider compounds allowing free screening against 40 different targets (or protein families) that are part of the DUD virtual screening dataset.