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Provides accurate and fast calculations for in-silico computation of pKa values. MoKa implements this approach using an algorithm based on descriptors derived from GRID molecular interaction fields. MoKa was trained using a very diverse set of more than 25000 pKa values. This package provides a graphical interface for predictions, containing tautomer check, batch mode for multi-structure files, integrated structure editor and cut and paste from ISIS/Draw (for Windows version). MoKa also proposes command line tools for advanced users.
Predicts pK(a) values for drug-like molecules. Epik can use this capability in combination with technology for tautomerization to adjust the protonation state of small drug-like molecules to automatically generate one or more of the most probable forms for use in further molecular modeling studies. Epik can process large databases of drug-like molecules to provide information on protonation states. Extensions to the well-established Hammett and Taft approaches are used for pK(a) prediction, namely, mesomer standardization, charge cancellation, and charge spreading to make the predicted results reflect the nature of the molecule itself rather just for the particular Lewis structure used on input. In addition, an iterative technology for generating, ranking and culling the generated protonation states is employed.
Specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar is an ab initio quantum chemical program that focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local second-order Moller-Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition-metal-containing systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling.
Calculates the accurate acidic and basic pKa values (negative logarithms of acid-base ionization constants) for organic compounds, in most cases, within an error of 0.25 pKa units. pKalc calculation can be performed for any organic compound, including aromatics, mono and polyheteroaromatics, and small peptides. The applied logarithm, adapted after Hammett and Taft takes into account all necessary electronic, steric and other effects and relies on an extended database of almost a thousand equations. pKalc predicts acidic and basic pKa values before synthesis, such as in diversity calculations for combinatorial chemistry, in quantitative structure-activity relationship (QSAR), in evaluating the synthesis possibilities, or in characterizing substance libraries. It is also helpful in situations when compounds are poorly soluble or may decompose in a water solution, as well as in the case of pKa values which are too high or too low.
Streamlines data access and analysis from a broad mixture of in-house and in licensed databases, reports, literature, and computational results by providing a wide array of tools for medicinal chemists, biologists, modelers, and Information Technology (IT) professionals. Seurat is optimized specifically for small molecule screening, hit-to-lead, lead optimization, and preclinical analysis. This tool can: (1) Compound and assay registration; (2) Search and query chemical, physical, and biological properties; (3) Elevate hits to leads, lead optimization, and pharmacokinetics (PK) analyses, and more.
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