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Bioinformatics Vol. 16 no. 9 2000
Pages 845-846
© 2000 Oxford University Press

Applications Note

TRITON: in silico construction of protein mutants and prediction of their activities *

Martin Prokop 1, Jií Damborský 1 and Jaroslav Koa 1,

1 Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic

Received on July 7, 1999 ; revised on November 2, 1999 ; accepted on November 8, 1999

Motivation: One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization.

Results: The graphical program TRITON has been developed for modelling protein mutants and assessment of their activities. Protein mutants are modelled from the wild type structure by homology modelling using the external program MODELLER. Chemical reactions taking place in the mutants active site are modelled using the semi-empirical quantum mechanic program MOPAC. Semi-quantitative predictions of mutants activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of active site residues during the reaction. The program TRITON offers graphical tools for the preparation of the input data files, for calculation and for the analysis of the generated output data.

Availability: The program TRITON can run under operating systems IRIX, Linux and NetBSD. The software is available at http://www.chemi.muni.cz/lbsd/triton.html.

Contact: triton{at}chemi.muni.cz

* Dedicated to Professor Milan Kratochvíl on the occasion of his 75th birthday.

To whom correspondence should be addressed.


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