SimBioSys is a Toronto based chemistry software company focusing on structure based drug discovery

Drug discovery

In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery...

 and retrosynthetic analysis

Retrosynthetic analysis

Retrosynthetic analysis is a technique for solving problems in the planning of organic syntheses. This is achieved by transforming a target molecule into simpler precursor structures without assumptions regarding starting materials. Each precursor material is examined using the same method. This...

 tools. It has established a strong reputation as one of the leading developers of flexible docking

Molecular docking

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex...

 applications, virtual screening

Virtual screening

Virtual screening is a computational technique used in drug discovery research. By using computers, it deals with the quick search of large libraries of chemical structures in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or...

 methods and computer aided organic synthesis design.

Areas of Expertise

Founded by a group of computer scientists and chemists, SimBioSys combines sophisticated search algorithms, machine learning

Machine learning

Machine learning, a branch of artificial intelligence, is a scientific discipline concerned with the design and development of algorithms that allow computers to evolve behaviors based on empirical data, such as from sensor data or databases...

 techniques and informatics

Information technology

Information technology is the acquisition, processing, storage and dissemination of vocal, pictorial, textual and numerical information by a microelectronics-based combination of computing and telecommunications...

 approaches with chemical knowledge and modelling.

Products

• 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
  Ligand
  In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
  
   in proteins' binding pockets. The application uses SimBioSys' proprietary scoring function
  Scoring functions for docking
  In the fields of computational chemistry and molecular modelling, scoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent interaction between two molecules after they have been docked...
  
  . 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
  Playstation 3 cluster
  The considerable computing capability of the PlayStation 3's Cell microprocessors has raised interest in using multiple, networked PS3s for various tasks that require affordable high-performance computing.- PS3 Clusters :...
  
   technology.
• LASSO - A similarity based virtual screening
  Virtual screening
  Virtual screening is a computational technique used in drug discovery research. By using computers, it deals with the quick search of large libraries of chemical structures in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or...
  
   tool that uses elements of eHiTS scoring function to identify bioactive molecules in large libraries of compounds.
• ARChem - A retrosynthetic analysis
  Retrosynthetic analysis
  Retrosynthetic analysis is a technique for solving problems in the planning of organic syntheses. This is achieved by transforming a target molecule into simpler precursor structures without assumptions regarding starting materials. Each precursor material is examined using the same method. This...
  
   tool that searches for possible synthetic routes from commercially available starting materials to target molecules.
• CheVi - SimBioSys' 3D molecular visualization software.

Partnerships

SimBioSys maintains marketing partnership with KeyModule. It distributes the UK based company's lead design tool, SPROUT, as well as other products.

See also

• Molecular docking
  Molecular docking
  In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex...
  
  
• Scoring functions
  Scoring functions for docking
  In the fields of computational chemistry and molecular modelling, scoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent interaction between two molecules after they have been docked...
  
  
• Virtual screening
  Virtual screening
  Virtual screening is a computational technique used in drug discovery research. By using computers, it deals with the quick search of large libraries of chemical structures in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or...
  
  
• Drug design
  Drug design
  Drug design, also sometimes referred to as rational drug design or structure-based drug design, is the inventive process of finding new medications based on the knowledge of the biological target...
  
  
• Retrosynthetic analysis
  Retrosynthetic analysis
  Retrosynthetic analysis is a technique for solving problems in the planning of organic syntheses. This is achieved by transforming a target molecule into simpler precursor structures without assumptions regarding starting materials. Each precursor material is examined using the same method. This...
  
  
• Cell microprocessor
  Cell microprocessor
  Cell is a microprocessor architecture jointly developed by Sony, Sony Computer Entertainment, Toshiba, and IBM, an alliance known as "STI". The architectural design and first implementation were carried out at the STI Design Center in Austin, Texas over a four-year period beginning March 2001 on a...
  
  

External links

• SimBioSys official site
• SimBioSys-Blog official blog site
• ARChem Route Designer presentation presentation on ARChem by Antony Williams
• Free Virtual Screening Service on ChemSpider; LASSO virtual screening was integrated with ChemSpider
  ChemSpider
  ChemsSpider is a free chemical database, owned by the Royal Society of Chemistry.-Database:The database contains more than 26 million unique molecules from over 400 data sources including those listed below.* A-L: EPA DSSTox, U.S...
  
   compounds allowing free screening against 40 different targets (or protein
  Protein
  Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
  
  families) that are part of the DUD virtual screening dataset.