Day: February 22, 2017

Unix Shell Programming Notes. Part I

/ Danilo Roccatano / 1 Comment

UNIX is basically a simple operating system, but you have to be a genius to understand the simplicity.
Dennis Ritchie

Shell commands can be combined in script files that perform complex actions. In this first article, a concise introduction to shell programming (focusing on the csh shell) is given. In the second part, I will provide some examples of complex scripting for different applications. For other types of shells, the reader can consult comprehensive textbooks that are listed at the end of this article.

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Yet Another Introduction To LINUX

/ Danilo Roccatano / Leave a comment

What is Linux?

Linux is a free and open source operative system (OS) derived from the Unix OS. It is created by Linus Torvalds. Initially, it was developed for personal computer but now it is diffused on almost all the existing computer architecture. The OS is freely available in different software distribution assembled by commercial or public companies. These distros regularly release freely available open-source Linux distributions in the form of a downloadable CD, DVD or even memory stick bootable images for the easy installation and customization. The reader is recommended to try to install her own version of Linux using one of the distributions (see a list at the end of the chapter). For scientific applications, the Scientific Linux is recommended since it is customized for the use in academic and research institutions and contains most of the open source scientific packages.

In this chapter, only a short introduction to the operative system Linux is provided. The reader is encouraged to deepen her knowledge on the topic by consulting more detailed tutorials or books guide suggested at the end of the chapter.

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Protein Engineering​ and Directed Evolution

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Phytase

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  1. A. Shivange, U. Schwaneberg, D. Roccatano. Conformational dynamics of active site loop in Escherichia coli phytase. Biopolymers. 93(11), 994–1002, (2010).

Monooxygenase P450 BM3

 Figure.

  1. S. Wong, N. Wu, D. Roccatano, M. Zacharias and U. Schwaneberg. Sensitive assay for laboratory evolution of hydroxylases toward aromatic and heterocyclic compounds. J. Biomol. Screen, 10, 246-252 (2005).
  2. Nazor, S. Dannennmann, R. Obeg Adjei, Y. B. Fordjour, T. I. Ghampson, M. Blanusa, D. Roccatano, U. Schwaneberg. Laboratory evolution of P450 BM3 for mediated electron transfer yields and activity-improved & reductase-independent variant. Protein Eng. Des. Sel., 21(1), 29-35, (2008).
  3. K. L. Tee, D. Roccatano, S. Stolte, J. Arning, B. Jastorff, U. Schwaneberg. Ionic liquids as cosolvents for biotransformation catalyzed by P450 BM-3. Green Chem., 10, 117-123, (2008).

Studies of preferential solvation of peptides and proteins in solution

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Chemical environment (pH, salts, co-solvents) plays an important role in the stabilization of secondary structure forming peptides and proteins in solution. The presence of co-solvent in aqueous solution can increase the structural stability as well as to promote denaturation or conformational changes. Continue reading →

Study of structural and dynamical properties of peptides in solutions

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The recent progress on time-resolved optical spectroscopy and FRET techniques have opened new exciting perspectives to the understanding the short timescale dynamics of peptides in solution. In fact, experimental data provided by these measurements can be directly compared with the results of computer simulations. Continue reading →