Docking Software, Now With Inhibition Constant Calculator. On-line Testing Is Launched

Quantum Pharmaceuticals is a technology leader in Computer Aided Drug Design and Computational Chemistry areas. Quantum Pharmaceuticals serves the life sciences industry and research community by providing flexible molecular docking software, compound profiling and selectivity testing services , virtual screening services and other top-of-the-line computational chemistry and computer aided d

Quantum Pharmaceuticals, a developer of breakthrough computer aided drug design and computational chemistry technologies, presents new free web service: on-line inhibition constant calculator as a showcase for its new docking software.

An accurate determination of inhibition constant for protein-ligand complexes plays a critical role in modern drug discovery describing binding interaction.

A binding interaction may mean that the ligand inhibits the protein's function or acts as an agonist. Docking is most pertinent to the field of drug design?most drugs are small molecules, and using a computational approach allows researchers to quickly screen large libraries of databases of compounds for virtual screening against protein targets such as, e.g., HIV reverse transcriptase. For example, virtual screening and related combinatorial chemistry techniques are particularly important in searching for new antibiotics as strains of resistant bacteria increasingly appear due to overuse of antibiotics. Traditional discovery of drug candidates occurs by chance or through painstaking work in the lab. Finding active compounds in common way may take several years and millions of dollars.

Notwithstanding the fact that there are quite a lot of docking software products currently presented on the market a creation of Quantum docking is a milestone of whole area.

The Quantum computer aided drug design and computational chemistry technology was developed using a new paradigm in molecular modeling ? applying quantum and molecular physics instead of statistical scoring-function-like and QSAR-like methods used by the majority of competitive software tools. It enables for highly effective industrial computer aided drug design.

The problem associated with the competitive knowledge based approaches is a small size of the training set used in their program parameters "training" (about 200 complexes, which is far less than the number of known complexes (about 2500)). While the performance of the their force fields can be awesome for complexes with chemical structure similar to that used in training (that happened when they achieved this correlation), the power of the first principles methods can be clearly judged by their ability to predict absolutely novel types of interactions and therefore inhibitors. For example Quantum do not train its free binding energy to reproduce the experimental binding affinities and at the same time our test set consists of more than 900 complexes. That is the main problem with scoring function based software.

Now researchers have a guaranty that if they take randomly complex # 901 which will be absolutely novel they will get the same quality of
calculations as they had previously, scoring will never give such guaranties.

So it is very difficult to identify inhibitors of novel classes using such knowledge based approaches. In the same time inhibitors of the novel classless and novel mechanisms of action are the top interest of pharmaceutical companies.

Thus Quantum docking software is a resolution of a long standing problem in computer aided drug design-performing molecular modeling and calculations with the level of accuracy comparable with in-vitro test.
Inhibition constant value prediction module being a part of Quantum docking software is available on http://q-lead.com/cnt/quantum for free calculations.

The demo version of Quantum docking can be downloaded at http://www.q-pharm.com/home/contents/drug_d/protein-ligand-docking-software

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by Maxim Kholin (few years ago!)

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