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In Silico

Section: New Tools, Products and Technologies     View all sections


11 Startups Using Quantum Theory To Accelerate Drug Discovery

   by Andrii Buvailo    1807
11 Startups Using Quantum Theory To Accelerate Drug Discovery

Molecular mechanics (MM) is a traditional computational approach when it comes to modeling in synthetic organic chemistry, medicinal chemistry and versatile aspects of drug design. However, MM methods have significant limitations, for example, when used to study electron-based properties within the drug-receptor microenvironment. Quantum mechanical (QM) methods allow to substantially increase the accuracy of predictions and provide much more relevant models of chemical and biological objects and their interactions, but QM methods are extremely (often prohibitively) computationally costly.

However, a series of advancements over recent years allowed to expand horizons in this direction, for example, the emergence of density functional theory (DFT), the overall increase in the computation power and the emergence of distributed cloud-based computational infrastructures.

Confluence of Technologies Can Bring “Virtual Pharmacology” to the Next Level

   by Andrii Buvailo    1577
Confluence of Technologies Can Bring “Virtual Pharmacology” to the Next Level

In 1970-80s, the idea of virtual screening was regarded as a conceptual way to substitute costly and time-consuming experimental “screen-everything-you-have” approaches with a much faster and cheaper predictive modelling to cherry-pick only the best molecules for subsequent synthesis and validation in a lab. A great number of computational tools and approaches emerged, aiming at “pre-screening” new promising molecules, so called “hits”, or augmenting experimental screening programs to optimize efforts.

Presenting a New Paradigm for Drug Discovery: Combining Computational Biophysics and AI through MatchMaker

   by Naheed Kurji    1148
Presenting a New Paradigm for Drug Discovery: Combining Computational Biophysics and AI through MatchMaker

In this Special Perspective, our fourth in an ongoing series, we will be presenting MatchMaker™, a novel deep proteome screening technology that we have developed and validated over the past 2 years to identify DTIs. MatchMaker builds on Cyclica’s passions of combining protein, chemistry, and genomic data, and augmenting it with high performance computing and algorithm development supported on the cloud.

ConstruQt - a Reliable Molecular Structure Predictor in the Cloud

   by Peter Jarowski    738
ConstruQt - a Reliable Molecular Structure Predictor in the Cloud

Since August Kekulé’s proposal for the tetrahedral configuration of carbon or his more famous realization that benzene was a cyclic molecule, a snake biting its tale, molecular structure has been the leading consideration for the design of new molecules as drugs or performance materials. For the former, it is said that 70% of drug design is based on molecular shape with the remainder attributed to electrostatic or non-bonded interactions.

Structural chemistry began around the 1860 with these dual assignments by Kekulé but it wasn’t until one hundred years later with Allinger’s initial force field approaches that the first classical molecular mechanics (MM) models became available to make computer-assisted prediction of molecular structure. These models themselves are based on principles derived by Robert Hooke, a contemporary of Isaac Newton, in the mid 17th century with additional layers from van der Waals (19th century) etc.

Navigating In REAL Chemical Space To Find Novel Medicines (Now 3.8 Billion Molecules)

   by Andrii Buvailo    3178
Navigating In REAL Chemical Space To Find Novel Medicines (Now 3.8 Billion Molecules)

[Latest update: 27.07.2018]

February 6 2018 will be marked in history as the day when an automobile embarked on a million year trip into far space. On that day, Falcon Heavy, the 230ft megarocket, successfully launched from Cape Canaveral, Florida, bringing on board Elon Musk’s personal Tesla Roadster with a crash test dummy called 'Starman' strapped into the driver's seat.

"The imagery of it is something that's going to get people excited around the world." says Elon Musk, a guy who literally revolutionized the area of space travel having developed and successfully tested first reusable rockets in the aerospace history, opening new horizons for cosmos explorations.

While advances in aeronautics are making news headlines daily, a much quieter scientific revolution is also happening in the area of “chemical space” explorations -- the one which might soon uncover novel medicines to cure diseases.