Search results for "Computational biology"
showing 10 items of 1237 documents
Design of bioactive and structurally well-defined peptides from conformationally restricted libraries
2004
Libraries of peptides and proteins can be categorized according to the function of their origin in gene- and synthetic-based libraries. Both kinds of libraries have the potential to generate the same grade of molecular diversity, although the limits imposed by the synthetic methods have been lately a matter of discussion. However, the use of synthetic strategies allows incorporation of non-natural amino acids. The development of canfonnallonally restricted synthetic peptide libraries can be considered as a point of convergence of the two methodologies. In these libraries the diversity is grafted into scaffolds that are defined by stable secondary structural motifs, and the deconvolution pro…
In vivophage display: identification of organ-specific peptides using deep sequencing and differential profiling across tissues
2020
ABSTRACTIn vivophage display is widely used for identification of organ- or disease-specific homing peptides. However, the currentin vivophage biopanning approaches fail to assess biodistribution of specific peptide phages across tissues during the screen, thus necessitating laborious and time-consuming post-screening validation studies on individual peptide phages. Here, we adopted bioinformatics tools used for RNA sequencing for analysis of high throughput sequencing (HTS) data to estimate the representation of individual peptides during biopanningin vivo. The data fromin vivophage screen were analyzed using differential binding – relative representation of each peptide in the target orga…
Validation strategies for antibodies targeting modified ribonucleotides
2020
Chemical modifications are found on almost all RNAs and affect their coding and noncoding functions. The identification of m6A on mRNA and its important role in gene regulation stimulated the field to investigate whether additional modifications are present on mRNAs. Indeed, modifications including m1A, m5C, m7G, 2′-OMe, and Ψ were detected. However, since their abundances are low and tools used for their corroboration are often not well characterized, their physiological relevance remains largely elusive. Antibodies targeting modified nucleotides are often used but have limitations such as low affinity or specificity. Moreover, they are not always well characterized and due to the low abun…
Classification of Complex Molecules
2009
Algorithms for classification and taxonomy based on criteria, e.g., information entropy and its production are proposed. In molecular classification, the feasibility of replacing a given molecule (e.g, anaesthetic) by similar ones in the composition of a complex drug is studied. Some local anaesthetics currently in use are classified using characteristic chemical properties of different portions of their molecules. In taxonomy, the detailed comparison of the sequences (primary structures) of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree for some species, e.g. the 1918 influenza virus. The method is applied to the classifications of: (1) …
A fast algorithm for the exhaustive analysis of 12-nucleotide-long DNA sequences. Applications to human genomics
2004
We have developed a new algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences. It is fast enough as to be used at a genomic scale running on a standard personal computer. As an example, we apply the algorithm to compare the number of all 12-nucleotide long words in human chromosomes 21 and 22, each of them more than 33 million nucleotides long. Sequences that are chromosome specific are detected in less than 2 minutes, being analyzed any pair of chromosomes at a rate of 45 millions of nucleotides (45 Mb) per minute. The size of the words is long enough as to allow further analyses of all significant sequences using conventional database searche…
Analysis of the proteins involved in the structure and synthesis of the cell wall of Ustilago maydis
2008
Abstract A study of the proteins involved in the synthesis and structure of the cell wall of Ustilago maydis was made by in silico analysis of the fungal genome, with reference to supporting experimental evidence. The composition of the cell wall of U. maydis shows similarities with the structural composition of the walls of Ascomycetes, but also shows important differential features. Accordingly, the enzymes involved in the synthesis of the U. maydis wall polysaccharides chitin and β-1,6 glucans displayed some differential characteristics. The most salient difference in protein composition was the predicted absence of Pir proteins, an important class of proteins present in the Ascomycetes.…
Nucleic Acids and Nuclear Proteins
1994
DNA deserves the most attention in any book dealing with molecular variety in animals. The complete genetic information of the organism is encoded in the order of the bases, and with it also is the whole spectrum of genetically determined variation within and between individuals. One can view DNA as a text in which each of the four letters at each position has a unique meaning. Some information and variety is lost en route from the DNA via RNA to the proteins and the complex morphological and physiological characters because only part of the DNA is transcribed into RNA, and not all RNA codes for proteins; furthermore, the genetic code is degenerate and the 64 possible triplet codons define …
Chapter 2 Biosynthesis in Rauwolfia serpentina Modern Aspects of an Old Medicinal Plant
1995
Publisher Summary This chapter discusses a research on Rauwolfia , which was achieved after the generation of a cell suspension with extraordinary growth characteristics and physiological behavior. The investigations demonstrated that a range of techniques is now available for the clarification of complete metabolic pathways, provided that the appropriate efficient biological system is available. The isolation and identification of each single enzyme have almost become routine, even if an extremely sensitive protein analytic technique is necessary when several kilograms of fresh plant cells are reduced to a few micrograms of homogenous protein. The successful identification of a total of 20…
Quantification of DNA and RNA: a Quantitative Visual Comparison
2002
The analytical procedure for the quantification of DNA and RNA described is the quantitative visual comparison of an unknown sample with known standards. This is quick and easy to do, suitable for amounts of sample as small as 10 ng. Keywords: DNA; RNA; rapid quantification
Activation of Mitochondria-Driven Pathways by Artemisinin and Its Derivatives
2014
Mitochondria have recently emerged as promising agents for cancer therapy. Of particular interest and potential clinical relevance are agents that target these organelles, promoting cell death. There are literally thousands of compounds that act on mitochondria and destabilise them. Of these, naturally occurring compounds are particularly interesting, since they are often more ‘biocompatible’; besides, natural compounds can be lead drugs for the design of novel and more efficient anti-cancer agents. In this paper, we focus on the natural product artemisin and its semisynthetic derivatives, and document the molecular mechanism of their activity and their potential use as clinically relevant …