Publications

The program TRITON:
Prokop, M., Adam, J., Kriz, Z., Wimmerova, M., Koca, J. 2008: TRITON: a graphical tool for ligand-binding protein engineering Bioinformatics 24: 1955-1956. Full text available (Open Access Article)

Prokop, M., Damborsky, J., Koca, J., 2000: TRITON: in silico construction of protein mutants and prediction of their activities. Bioinformatics 16: 845-846.

Damborsky, J., Prokop, M., Koca, J., 2001: TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences 26: 71-73.

Concept of computational site-directed mutagenesis:
Damborsky, J., Bohac, M., Prokop, M., Kuty, M., Koca, J., 1998: Computational site-directed mutagenesis of haloalkane dehalogenase in position 172. Protein Engineering 11: 901-907.

The program MODELLER:
Sali, A., Blundell, T. L., 1993: Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 234: 779-815.

The program MOPAC:
Stewart, J.J.P., 1990: MOPAC - A semiempirical molecular-orbital program. Journal of Computer-Aided Molecular Design 4: 1-45.

The routine DRIVER:
Cernohorsky, M., Kuty, M., Koca, J., 1997: A multidimensional driver for quantum chemistry program MOPAC. Computers and Chemistry 21: 34-44.

The program AutoDock:
Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. and Olson, A.J., 1998: Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function Journal of Computational Chemistry 19: 1639-1662.

Computer modelling of dehalogenation reaction:
Damborsky, J., Kuty, M., Nemec, M., Koca, J., 1997: A molecular modeling study of the catalytic mechanism of haloalkane dehalogenase. 1. Quantum mechanic study of the first reaction step. Journal of Chemical Information and Computer Science 37: 562-568.

Kuty, M., Damborsky, J., Prokop, M., Koca, J., 1998: A molecular modeling study of the catalytic mechanism of haloalkane dehalogenase. 2. Quantum mechanic study of complete reaction mechanism. Journal of Chemical Information and Computer Science 38: 736-741.

Bohac, M., Nagata, Y., Prokop, Z., Prokop, M., Monincova, M., Tsuda, M., Koca, J., Damborsky, J., 2002: Halide-Stabilizing Residues of Haloalkane Dehalogenases Studied by Quantum Mechanic Calculations and Site-Directed Mutagenesis. Biochemistry 41: 14272-14280.

Application of TRITON in Comparative Binding Energy Analysis:
Kmunicek, J., Bohac, M., Luengo, S., Gago, F., Wade, R.C., Damborsky, J., 2003: Comparative Binding Energy Analysis of Haloalkane Dehalogenase Substrates: Modelling of Enzyme-Substrate Complexes by Molecular Docking and Quantum Mechanical Calculations. Journal of Computer-Aided Molecular Design 17: 299-311.