Calculators and Predictors

High-quality physico-chemical calculations & predictions for drug discovery

The behavior and effect of drugs on the human body are governed by the drugs molecular structure. This behaviour can be linked to important physico-chemical properties of the drug molecule. Optimizing these properties play crucial role in the early phases of drug discovery and design.
The component offers wide range of chemical calculations, available from multiple endpoints with great availability, consistency and integration options. A brief summary of the available plugins are listed below. Extensive API and training options provide further possibilities for integration and customization.

Elemental Analysis

Chemical properties like molecular mass, elemental composition, etc - are the simplest descriptors for molecules. Elemental Analysis provides these descriptors as separate calculations. Mass spectrum calculation (isotope distribution) with a displayed spectrum is also available. Documentation

Elemental Analysis

Protonation bundle

The influence of acid-base dissociation constant (pKa) for pharmacokinetik properties is well-established in scientific literature and in practice. Knowing the pKa values and major ionized forms at a given pH becomes especially important in those physiological cases where the ionization of the drug compound affects the rate at which it can diffuse through biological membranes and barriers - like the blood-brain barrier for example.

ChemAxon’s Protonation bundle provides:

  • Highly-accurate calculation of pKa values. Along with the predicted pKa values comes a display of microspecies distribution chart. Documentation
  • Calculation of major microspecies forms at a given pH value. Documentation
  • Calculation of isoelectric point (the pH at which the net charge of the molecule is zero). Documentation

ChemAxon's pKa calculation

Partitioning bundle

Partition coefficients - logP, and its pH-dependent pair, logD - are crucial in estimating the distribution of drugs in the human body. Drugs with higher partition coefficients modelled in an octanol/water system are more likely to be distributed in the hydrophobic tissues like blood. However, molecules with low partition coefficients can mostly be found in lipophilic areas of the human body, like lipid bilayers of cells. The quality of the logP/logD prediction can be enhanced by incorporating measured logP/logD data through training.
HLB (Hydrophil-Lipophil Balance) number is another descriptor for characterizing lipophilicity/hydrophilicity, originally used for characterizing surfactants.

The Partitioning calculator group covers:

  • The calculation of logP using sound methods published in the literature. Documentation
  • Surely it includes the calculation of logD (pH-logD plot) for your molecules. Documentation | Try it now
  • The calculation of the HLB (hydrophil-lipophil balance) number using various methods from the literature. Documentation

logp calculation

Aqueous Solubility

Drug solubility in water is one of the most important parameters for optimization in drug design. Low aqueous solubility is a major problem encountered during formulation of new drugs, as every compound must be present in the form of a solution at its site of absorption in order to be effective.

ChemAxon’s Aqueous Solubility predictor is able to predict intrinsic thermodynamic and pH-dependent solubility in water. It is also able to determine qualitative solubility category based on predefined solubility thresholds. Documentation | Try it now

solubility

Nuclear Magnetic Resonance (NMR)

Nuclear Magnetic Resonance spectroscopy is mainly used to elucidate unknown molecular structures coming from experimental measurements. Predicting NMR spectra for a set of possible structures and comparing them with experimental data is a well established approach to facilitate structure elucidation.

ChemAxon’s NMR predictor is able to predict 1H and 13C spectra for organic molecules that are composed of the most frequent elements (H, C, N, O, F, Cl, Br, I, P, S, Si, Se, B, Sn, Ge, Te and As). Documentation

NMR Predictor

Isomers bundle

Molecular libraries can often lack proper stereoisomer information, which can lead to ambiguous representation in 3D. Enumerating stereoisomers are therefore important for virtual screening applications, e.g. docking or 3D QSAR.

Tautomerization is also a specific intra-molecular conversion, which can affect identification, searching, and properties of molecules. The proper treatment of molecules that can tautomerize, is an important problem to solve.

The Isomers bundle contains tools for effective stereoisomer and tautomer generation:

  • The Stereoisomer generator is able to enumerate isomers based on tetrahedral and double bond stereocenters present in the molecule. The generator is able to restrict the number of generated isomers by protecting existing centers or by filtering out invalid 3D structures generated. Documentation | Try it now
  • The Tautomer generator is able to enumerate different tautomeric forms and sets of tautomers. These forms and sets can be used for chemical searching, screening and property prediction applications too. Documentation | Try it now

isomers

Structural Calculations & Predictions

ChemAxon’s Structural Calculations & Predictions provide such calculations, including: Hydrogen Bond Donor/Acceptor (HBDA), topological and geometrical descriptors, basic tools for 3D chemistry (conformer generation, 3D Alignment and Molecular Dynamics), and different electron-structural property (like partial charge distribution, refractivity, resonance etc), and calculations.Documentation

geometry