In Silico methods

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In silico is an expression that means "performed using a computer simulation" and was coined in 1989 during the workshop "Cellular Automata: Theory and Applications" in Los Alamos, New Mexico by a mathematician from National Autonomous University of Mexico (UNAM).

In silico models for predicting toxicological, biological and physico-chemical properties are models able to find relations between particular characteristics of molecules and the property of interest. Example of in silico methods are: (Q)SAR, Read-Across and Virtual Screening.

Quantitative Structure-Activity Relationship (QSAR) are computer-based models for the prediction of toxicological, biological and physico-chemical properties. QSAR models aim at establishing, if it exists, the relationship between structural-derived properties of chemicals and their properties, such as toxicity. For the relationship between the activity and the chemical information a mathematical function is used. The chemical information can be given by chemical descriptors or fragments. Many thousands of chemical descriptors have been proposed, constitutional, geometrical, physico-chemical, topological, etc.
In the specific case of the evaluation of a qualitative relationship, for instance between the presence of a certain chemical fragment and the occurrence of a certain toxicity effect, the typical name is structure-activity relationship (SAR). (Q)SAR is used sometimes to refer to both QSAR and SAR. Here we will present QSAR and SAR together, using the acronym QSAR.

Read-across is a very simplified version of QSAR model. Basically, the property of one or few chemicals is predicted on the basis of one or more similar compounds, using or not some chemical descriptors.

Virtual screening are docking simulation based methods used to evaluate the binding between a chemical compound and a biological macromolecule, such as a protein.

 

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Related FAQ

What is ORCHESTRA?

ORCHESTRA is an EU project, funded to disseminate recent research on computer-based in silico methods for evaluating the toxicity of chemicals.

•• In silico methods make it possible to test large numbers of chemicals (as required by EU REACH legislation) while reducing the numbers of tests on animals.

The aim of the project is therefore to promote wider understanding, awareness and appropriate use of in silico methods.

Learn more here
 

How can this project/site help me?

If you are not familiar with in-silico methods, download the introductory leaflet, study the online course and read the ORCHESTRA e-book “Theory, guidance and applications on QSAR and REACH”;
for users of in silico / QSAR methods, there are resource links on this site;
to hear discussion of the issues and priorities, watch the documentary video;
if you want to know more, keep an eye on the posted events & activities
 

What are in silico methods?

In silico methods simply means computer-based methods.  In this context they are computer-based methods for assessing the toxicity of chemicals.  

In silico methods involve using databases of existing experimental data on the toxicity of chemicals.  That data is used to predict the toxicity of chemicals which are similar to those already tested.   The advantage of in silico methods is that they make it possible to assess the toxicity of large numbers of chemicals quickly using a database and software on a desktop computer, whereas assessments were formerly only possible from long and expensive tests in laboratories.  However, the main limitation is in the amount of existing data available; much is held by industry as confidential, and in some areas (such as long term toxicities for mammals) the amount of existing data of high quality is limited.  

In silico methods are widely used (including by regulators in the US) to screen and identify chemicals for priority testing in the laboratory. They are also used in addition to available laboratory data to generate a stronger ‘weight of evidence’.  In silico methods include QSAR models, ‘Read across’ and Virtual Screening.

The term in silico contrasts with in vivo and in vitro.  In vivo methods involve testing chemicals on living organisms, including invertebrates, fish and animals.  In vitro methods involve test-tube research, where (for example) instead of putting the chemical on the skin or in the eye of an animal, the chemical is put in a test tube with some living skin cells or eye cells taken from an animal.  Both in silico and in vitro methods are known as ‘alternative methods’.  In silico methods make use of existing data from in vivo and in vitro tests.

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