---------- Forwarded message ---------- From: Wilfried Langenaeker <[email protected]> Date: Wed, Jul 21, 2010 at 12:49 AM Subject: Silicos goes Open Source To: "Bryan Bishop" <[email protected]>
PRESS RELEASE: SILICOS NV PORTS ITS PROPRIETARY COMPUTATIONAL CHEMISTRY SOFTWARE INTO THE OPEN SOURCE DOMAIN On June 22, 2010, the Belgium-based computational chemistry company Silicos NV has made a strategic decision to port the majority of its proprietary software into the open source arena. The decision has been made to port all of these tools and the corresponding C/C++ API's into the Open Babel environment under a GNU GPL licensing scheme. This strategic decision will position Silicos NV as one of the leading computational chemistry services companies to support the open source business model. According to Hans De Winter, Silicos' CSO, 'the decision will allow Silicos to move forward rapidly on the expanding wave of open source software tools, and will significantly expand its possibilities of providing services to customers in the pharmaceutical and biotechnological industry.' About Silicos' proprietary software tools Spectrophores™ are Silicos' patented 3D-field descriptors. Spectrophores™ are a one-dimensional description of three-dimensional molecular properties, such as atomic electrostatic charges, atomic lipophilicity, atomic softness, atomic electrophilicity and shape. Spectrophores™ have been succesfully used for clients to build sophisticated QSAR models in combination with many statistical modelling algorithms like bayesian classification and support vector machines. Due to their numeric nature, Spectophores™ are well-suited for the calculation of self-organising maps. Pharao is Silicos' implementation of a pharmacophore-based alignment tool. It uses a Gaussian representation of pharmacophoric features and generates an alignment between pairs of a set of pharmacophores. The resulting match is quantified using different measures including a Tanimoto coefficient. Piramid is Silicos' software tool incorporating a shape-based alignment between pairs of molecules. Again, the resulting match is quantified using different measures including a Tanimoto coefficient. Finally, Cosmos™ is Silicos' patented technology for the design of novel molecules using an evolutionary algorithm and using user-specified scoring functions. The tool has been adapted to be used in a fragment-based discovery enviroment. It has been succesfully used in a number of drug discovery programs in which Cosmos™ was able to generate novel chemistry that has not been described before. The strength of Cosmos™ lies in its multi-objective optimisation algorithm as well as in the fact that virtually all kinds of scoring functions can be integrated. About Silicos NV Silicos NV is providing services in the field of computational chemistry and virtual screening. The company was founded in 2005 by two former employees of a major pharmaceutical company in Belgium and a former researcher at the ESAT-group of the Catholic University of Louvain. Silicos is a spin-out of the Catholic University of Louvain. For more information For more information regarding Silicos NV, please visit the website at www.silicos.com or contact Wilfried Langenaeker at +32 478 98 12 20. Silicos NV Wetenschapspark 7 B-3590 Diepenbeek Belgium www.silicos.com """ Silicos' virtual screening technology is based on a unique concept called Spectrophores™. These are descriptors reflecting all possible three-dimensional molecular properties which are involved in the binding of a drug to its receptor, including electrostatic potential, lipophilicity, softness, and shape. Cosmos™ is Silicos' platform for the in silico, de novo design of small molecules. The program serves as a fragment-based molecular optimization application, in which novel molecules are generated by combining fragments in a virtual synthesis step. These molecular structures are further optimized in single or multi-objective optimisation procedures. The evaluation of the quality of the molecules can be ligand-based or target-based which makes Cosmos™ a very flexible platform for de novo drug discovery. Pharao is a pharmacophore-based tool to score and align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimization problem introduced during alignment. SiMath is Silicos' open source API for statistical and mathematical data modeling. SiMath is C++ library which integrates several open source libraries into one library and which can easily included in other applications. """ """ De Novo design with Cosmos™ Cosmos™ is an acronym for Computational Optimization of Small Molecular Structures. It is a highly flexible in silico platform, based on a genetic algorithm for the evolution of molecules guided by one or more evaluation functions and fragment-based virtual synthesis. Evaluation functions can be ligand- and target-based. As in a classical in vitro setup, Cosmos™ is build round three main blocks: virtual synthesis, evaluation or virtual screening, and optimization. The process is illustrated in the flowchart above. In the virtual synthesis step, de novo molecules are developed from a set of predefined building blocks and connectivity rules. Both building blocks and connectivity rules have been extracted from known compounds. As such, the possibility that the virtual compounds actually are synthesized in a later stage is rather high. In the next step, the molecules are evaluated using a virtual screening function. The evaluation of the molecule can be based on any kind of function and is completely flexible to meet the project needs. Typical evaluators that have been tested, are docking, shape-based similarity, fingerprint similarity, and Spectrophore™ models. The optimization step can be either a single- or multi-objective optimization depending on the number of targets and different scoring functions. From the scores, molecules are selected for further participation in the evolutionary process. Genetic operators, like mutation and crossover, have been implemented again using the same building blocks and connectivity rules as defined in the virtual synthesis. This closes the loop and the process restarts. Example To illustrate the potential of Cosmos™, cisapride has been used as a test case. The crystal structure of cisapride was used a template structure and new virtually synthesised compounds were compared with the template using a shape-based scoring function. """ - Bryan http://heybryan.org/ 1 512 203 0507 ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
