PERL is an acronym for Practical Extraction and Report Language. This scripting language was initially developed by Larry Wall with the intent to extend the potentiality of the awk and sed program for text manipulation and for Unix system administration tool. It takes the best features of many other languages, such as C, sed, and awk. In addition, Perl supports both procedural and object-oriented programming. Perl is the most popular web programming language due to its capability with text manipulation and rapid development cycle. The same capabilities began a precious support to bioinformatician to data mining the rapid accumulation of a large amount of genetic information from the molecular biology research. Continue reading
Author: Danilo Roccatano
COMPUTER SIMULATIONS STUDIES OF PEPTIDES IN ORGANIC SOLVENTS AND COSOLVENTS: A SIMPLE DATABASE
SIMPEOS is a simple hypertextual database that provides a list of peptides that have been studied using molecular dynamics simulations in non-aqueous solvents. Continue reading
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The Molecular Dynamics Docking Method
Understanding the mechanisms of the molecular recognition has fundamental impacts in medicine and biotechnology. It plays an important role in discovering new drugs and in developing new biocatalyst. The theoretical study of these mechanisms has boosted the development of approximated but fast methods for screening large compound libraries and protein-protein complexes. Continue reading
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The AWK Programming Language
Awk is a powerful Unix tool. Its name derives from the surname initials of Alfred Aho, Peter Weinberger, and Brian Kernighan who originally designed it at Bell Labs in 1977. The program has a different version and implementations. A commonly used one is the gawk from the GNU (http://www.gnu.org/s/gawk/). According to the definition of one of its developer, Alfred. V. Aho: “AWK is a language for processing files of text. A file is treated as a sequence of records, and, by default, each line is a record. Each line is broken up into a sequence of fields so we can think of the first word in a line as the first field, the second word as the second field, and so on. An AWK program is a sequence of pattern-action statements. AWK reads the input a line at a time. A line is scanned for each pattern in the program, and for each pattern that matches, the associated action is executed.”
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Unix Shell Programming Notes. Part I
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
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
Phytase
- 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.
- 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).
- 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).
- 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).
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Studies of preferential solvation of peptides and proteins in solution
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
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Study of Structural and Dynamical Properties of Peptides in Solutions
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.
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Adsorption mechanism of an antimicrobial peptide on carbonaceous surfaces: A molecular dynamics study
Danilo Roccatano, Edita SarukhanyanThe Journal of Chemical Physics 146, 074703 (2017); doi: http://dx.doi.org/10.1063/1.4975689
Cover PagePeptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptake by living cells, and their high surface to volume ratio facilitates the adsorption of molecules of different nature. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutically agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A – Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surface through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalize Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to a loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus, into the interior of the CNT was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion.
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