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Chapter 1. Overview
The MoKa suite is a collection of tools for pKa prediction. The main program, MoKa, predicts quickly and accurately the pKa of a compound and is available both as command-line tool and as an easy-to-use graphical interface. The accuracy of the calculations can be extended by using Kibitzer, an advanced and fully automatic training system. Versus enables a quick evaluation of the accuracy of predicted pKa versus experimental pKa. Blabber is a command-line tool for protonation and deprotonation of a molecule at the given pH. Tauthor allows enumeration of possible tautomers of the input molecule.
1.1. Manual organization
This manual explains how to use MoKa and it is organized as follows:
Chapter 3 provides an overview of pKa calculations and of methods implemented in MoKa.
Chapter 4 describes how to use the MoKa graphical user interface.
Chapter 5 describes how to use the command-line version of MoKa.
Chapter 6 describes how to build customized pKa prediction models with Kibitzer.
Chapter 7 describes how to protonate and deprotonate structures with Blabber.
Chapter 8 describes how to enumerate tautomeric forms with TauThor.
Chapter 9 describes how to evalute the accuracy of pKa calculations with Versus.
1.2. Citing MoKa
The use of this product should be acknowledged in publications as:
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