BIOINFORMATICA PASCARELLA PDF

Knowledge and understanding: the course aims to provide the students with the theoretical knowledge essential to the understanding of data and information derived from bioinformatics analyses. Applying knowledge and understanding: through practical exercises under the guidance of the teacher, students will have the opportunity to acquire the skills necessary to perform analysis of biological data through the use of computers. Making judgments: During the course, students will be trained to interpret the results of computer analysis and to assess the degree of reliability of the evidence bioinformatics. Communication skills: through examples, students will learn how to communicate in a written paper consisting of text and images results and interpretations of bioinformatics analysis. Basic knowledge of biological macromolecules and the foundations of Biochemistry and Molecular Biology.

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Pascarella uniroma1. Si raccomanda di prendere appuntamento tramite messaggio di posta elettronica. R language. Molecular dynamics simulation unveils the conformational flexibility of the interdomain linker in the bacterial transcriptional regulator GabR from Bacillus subtilis bound to pyridoxal 5'-phosphate. PLoS One.

Nov 2. Mugosa, B. Hepatitis C virus genotype 3A in a population of injecting drug users in Montenegro: Bayesian and evolutionary analysis Archives of Virology, 6 , pp. Tramonti, A. Amidani, D. Milano, T. Structural properties of the linkers connecting the N- and C- terminal domains in the MocR bacterial transcriptional regulators Biochimie Open, 3, pp. Angelaccio, S. Data from computational analysis of the peptide linkers in the MocR bacterial transcriptional regulators Data in Brief, 9, pp.

Angeletti, S. Giovanetti, M. A bioinformatics analysis reveals a group of MocR bacterial transcriptional regulators linked to a family of genes coding for membrane proteins Biochemistry Research International, , art. Molecular mechanism of PdxR - A transcriptional activator involved in the regulation of vitamin B 6 biosynthesis in the probiotic bacterium Bacillus clausii FEBS Journal, 15 , pp. Di Salvo, M. The aspartate aminotransferase-like domain of Firmicutes MocR transcriptional regulators Computational Biology and Chemistry, 58, pp.

Conserved water molecules in bacterial serine hydroxymethyltransferases Protein Engineering, Design and Selection, 28 10 , pp. Facchiano, A. Prudente, S. Paiardini, A. Singh, R. Fullone, M. Insight into the structure-function relationship of the nonheme iron halogenases involved in the biosynthesis of 4-chlorothreonine - Thr3 from Streptomyces sp. OH and SyrB2 from Pseudomonas syringae pv. Bramucci, E. Serine hydroxymethyltransferase from the cold adapted microorganism Psychromonas ingrahamii: A low temperature active enzyme with broad substrate specificity International Journal of Molecular Sciences, 13 2 , pp.

Siglioccolo, A. Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface BMC Structural Biology, 11, art. Genomic distribution and heterogeneity of MocR-like transcriptional factors containing a domain belonging to the superfamily of the pyridoxal-5'-phosphate dependent enzymes of fold type I Biochemical and Biophysical Research Communications, 1 , pp. Structural adaptation of serine hydroxymethyltransferase to low temperatures International Journal of Biological Macromolecules, 46 1 , pp.

Severino, V. Structural analysis of toxic volkensin, a type 2 ribosome inactivating protein from Adenia volkensii Harm kilyambiti plant : Molecular modeling and surface analysis by computational methods and limited proteolysis International Journal of Biological Macromolecules, 45 4 , pp. Baldasseroni, F. Subunit interfaces of oligomeric hyperthermophilic enzymes display enhanced compactness International Journal of Biological Macromolecules, 44 4 , pp.

Maugini, E. Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes Computational Biology and Chemistry, 33 2 , pp. Tronelli, D. Structural adaptation to low temperatures - Analysis of the subunit interface of oligomeric psychrophilic enzymes FEBS Journal, 17 , pp.

Gianese, G. A consensus procedure improving solvent accessibility prediction Journal of Computational Chemistry, 27 5 , pp. Di Vincenzo, L. In silico analysis of the adenylation domains of the freestanding enzymes belonging to the eucaryotic nonribosomal peptide synthetase-like family FEBS Journal, 4 , pp. Brisdelli, F. Kinetic properties of native and mutagenized isoforms of mitochondrial alcohol dehydrogenase III purified from Kluyveromyces lactis Biochimie, 86 , pp.

Improvement in prediction of solvent accessibility by probability profiles Protein Engineering, 16 12 , pp. Threonine aldolase and alanine racemase: Novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes Biochimica et Biophysica Acta - Proteins and Proteomics, , pp.

Structural plasticity of thermophilic serine hydroxymethyltransferases Proteins: Structure, Function and Genetics, 50 1 , pp. Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes Proteins: Structure, Function and Genetics, 47 2 , pp.

Contestabile, R. L-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase: A subgroup of strictly related enzymes specialized for different functions European Journal of Biochemistry, 24 , pp. Structural adaptation of enzymes to low temperatures Protein Engineering, 14 3 , pp. Erba, F.

Selective inhibition of human mast cell tryptase by gabexate mesylate, an antiproteinase drug Biochemical Pharmacology, 61 3 , pp. Ruoppolo, M. Characterization of five new low-molecular-mass trypsin inhibitors from white mustard Sinapis alba L. Birolo, L. Cloning, expression, properties, and molecular modelling European Journal of Biochemistry, 9 , pp.

Zamparelli, C. Structure-function relationships in sorcin, a member of the penta EF- hand family. Interaction of sorcin fragments with the ryanodine receptor and an Escherichia coli model system Biochemistry, 39 4 , pp. Bonaccorsi Di Patti, M. Homology modeling of the multicopper oxidase Fet3 gives new insights in the mechanism of iron transport in yeast Protein Engineering, 12 11 , pp. Polticelli, F. The T-Knot motif revisited Biological Chemistry, 10 , pp. Ascenzi, P. Characterization of low-molecular-mass trypsin isoinhibitors from oil- rape Brassica napus var.

Leech antihemostatic proteins share the T-knot scaffold, a disulfide-reinforced structural motif Biological Chemistry, 11 , pp.

Pascarella, S. The structure of serine hydroxymethyltransferase as modeled by homology and validated by site-directed mutagenesis Protein Science, 7 9 , pp. Easy method to predict solvent accessibility from multiple protein sequence alignments Proteins: Structure, Function and Genetics, 32 2 , pp. Rossi, R. Fast-reacting thiols in rat hemoglobins can intercept damaging species in erythrocytes more efficiently than glutathione Journal of Biological Chemistry, 30 , pp.

Arnone, M. Stability of aspartate aminotransferase from Sulfolobus solfataricus Protein Engineering, 10 3 , pp. Mignogna, G. BSTI, a trypsin inhibitor from skin secretions of Bombina bombina related to protease inhibitors of nematodes Protein Science, 5 2 , pp. Toney, M. Conservation of amphipathic conformations in multiple protein structural alignments Protein Engineering, Design and Selection, 7 2 , pp.

Levin, J. Quantification of secondary structure prediction improvement using multiple alignments Protein Engineering, Design and Selection, 6 8 , pp. Similarity between serine hydroxymethyltransferase and other pyridoxal phosphate-dependent enzymes FEBS Letters, , pp. A data bank merging related protein structures and sequences Protein Engineering, Design and Selection, 5 2 , pp. Fattori, E. Site-Directed Mutagenesis in the Study of Serine Hydroxy methyltransf erase [Mutagenesi sito-specifica nello studio delta serina idrossimetiltrasferasi] Rendiconti Lincei, 1 2 , pp.

Pronet: A microcomputer program for predicting the secondary structure of proteins with a neural network Bioinformatics, 5 4 , pp. Cleavage: A microcomputer program for predicting signal sequence cleavage sites Bioinformatics, 5 1 , pp.

Martini, F. The primary structure of rabbit liver mitochondrial serine hydroxymethyltransferase Journal of Biological Chemistry, 15 , pp. Methods for identifying antigen determinants of proteins on the basis of primary structure Italian Journal of Biochemistry, 37 4 , pp.

The primary structure of rabbit liver cytosolic serine hydroxymethyltransferase. A simple microcomputer program for predicting the secondary structure of proteins Computer Methods and Programs in Biomedicine, 24 3 , pp. Doonan, S. The complete amino acid sequences of cytosolic and mitochondrial aspartate aminotransferases from horse heart, and inferences on evolution of the isoenzymes Journal of Molecular Evolution, 23 4 , pp. Elenco recapiti telefonici.

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