Alzheimer’s disease: Modeling current and potential targets
By the time we are 65, one in ten of us will have contracted Alzheimer’s disease. This rises to fifty ...
At Cresset we are proud of our combination of intuitive user interfaces and powerful underlying science. We take the time and thought to design our software so that it is as easy to use as possible. We want the interface to facilitate the science, not to get in the way.
Nonetheless, our software deals with complex computational chemistry, so it is never going to be entirely accessible to the casual user. Blaze, Spark and Forge are expert tools designed for specialists and to exploit them to their maximum potential we always recommend user training.
Many companies want the value of our software but cannot spare the personnel or the time to become experts. Cresset’s consulting services offers the chance to access our methods and the expertise of our consultants as and when you need them.
The most obvious and popular services to be outsourced are those that are complex, run infrequently or that require specialized equipment or high levels of computer power. This matrix classifies typical computational chemistry tasks by the complexity of their method and the computational power required.
|Easy method||Complex method|
Scoring new compounds on an existing model
Simple bioisostere replacement
SAR analysis (matched molecular pairs, activity cliffs)
|Computationally intensive||Virtual screening
|Protein field analysis
Library design and optimization
Virtual screening is a prime example of a technique that is often outsourced. It is run infrequently and takes very large amounts of computing resources. You can read more about outsourcing virtual screening in these recent blogs.
3D-QSAR is a method that is a less obvious candidate for outsourcing.
3D-QSAR actually uses modest amounts of computational resources. It can be run on a typical users’ desktop machine, or modern powerful laptop – I run mine on a small light laptop with an Intel Core-i7 processor, and can process even quite large data sets in reasonable time. The method is made available in easy-to-digest form within Forge, a powerful tool with a nice graphical user interface. So why outsource 3D-QSAR?
The answer comes down to the complexity of the method: it truly is a question of ‘the devil is in the detail’. While powerful statistical techniques can give seemingly miraculous results, once needs to be constantly aware of the potential issues which can arise – over-parameterized models, statistically questionable predictions, robustness to extrapolation rather than interpolation, and many more. Not to mention the complexities of conformational searching, molecular alignment, variations in binding modes across series, dealing with inconsistent biological data, etc.
Because of these inherent complexities in the methods, 3D-QSAR is a tool best handled by an expert, or at least in a consistent and ongoing way. By accessing 3D-QSAR through Cresset’s consulting services team, you gain not only the scientific methods, but also the services of an expert who uses the tool on a daily or weekly basis to solve real-world customer problems.
Overall I believe Cresset achieves a good balance between the provision of powerful science and making that science readily accessible and easily understandable.
Our consulting services offering enables all customers to benefit from hard core computational science without making the hard core investments in people and computers.
Consulting projects generate a combination of Cresset expertise and customer knowledge that can be very powerful. Many scientists have found it to be the ideal means to generate insight into existing project data and determine future research directions.