Silico tools

Cardiac models are amongst the most advanced in silico tools for bio-med-icine, and the above scenario is bound to become reality rather sooner than later. Both cellular and whole organ models have aheady matured to a level where they have started to possess predictive power. We will now address some aspects of single cell model development (the cars ), and then look at how virtual cells interact to simulate the spreading wave of electrical excitation in anatomically representative, virtual hearts (the traffic ). 

So much for the advantages. Virtual organs clearly have one major drawback they are models only. While this very nature of in silico technology is the core foundation for the benefits listed above, it also calls for a word of caution. It is imperative for in silico tools to be seen in the context of a whole range of scientific and research tools, and to never neglect that theoretical considerations will continue to need experimental validation. 

The information about internal and external validation for the model is used to evaluate the performance of the in silico tool. 

Milan C, Schifanella O, Roncaglioni A, Benfenati E (2011) Comparison and possible use of in silico tools for carcinogenicity within REACH legislation. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 29(4) 300-323... 

Marchant CA, Briggs KA, Long A (2008) In silico tools for sharing data and knowledge on toxicity and metabolism Derek for Windows, Meteor, and Vitic. Toxicol Mech Methods 18 177-187... 

Jacobs, M.N. (2004) In silico tools to aid risk assessment of endocrine disrupting chemicals. Toxicology, 205, 43—53. 

Part 3 Bioinformatics—In Silico Tools to Predict Drug Absorption... 

In this section, discussion of physicochemical profiling is limited to solubility, permeability, drug stability, and limited solid-state characterization (as we will see in Section 3.4, there are other physical-mechanical properties that must also be considered). For convenience, methods available for physicochemical profiling are discussed under the following categories computational tools (sometimes referred to as in silico tools), HTS methods, and in-depth physicochemical profiling.16... 

Fig. 14.9 Individual components of multidimensional optimization. This approach requires experimental compound profiling against key properties, which should be done on a designed compound subset to maximize information with a minimum number of molecules. These data are used to derive models for key properties, which are applied during the next design cycle. The results then led to augmented models. The process is characterized by a tight integration of in vitro and in silico tools for profiling compound series to guide chemical optimization.

In Silico Tools and In Vitro HTS Approaches to Determine Lipophilicity During the Drug Discovery Process... 

The LFER approach of Abraham was the most powerful method to predict partition coefficients in varied experimental conditions (for example, see [68-72]). In particular, since 1,2-dichloroethane and o-nitrophenyl octyl ether are good experimental substitutes for alkane, in silico tools were developed with LFER equations to predict log Pdce [73] or log Pnpoe [74, 75]. 

Hofacker, anclP.F. Stacller (Chapter 12) pursue a similar goal concerning functional nucleic acids and provide various in silico tools to predict RNA folding. 

The constant refinement of techniques for directed protein evolution also involves the development of increasingly sophisticated in silico tools. This co-evolution of experimental and computational methods enriches our toolkit for finding the sequence that fits. It is this mutual impact which makes ProSa a valuable component in designing both experiments and proteins. 

In Silico Tools for GPCR Anti-target Modeling... 

Two major in silico tools in vaccine design are based on two related but distinct strategies immunoinformatics-based immune epitope prediction and reverse vaccinology-based protective protein antigen screening. 

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