Biomedical subjects

Ivan Rossi

Publications and source records attributed to Ivan Rossi.

3 recordsLinked to original sources

PubMed2004

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues.

Detection of homologous proteins with low-sequence identity to a given target (remote homologues) is routinely performed with alignment algorithms that take advantage of sequence profile. In this article, we investigate the efficacy of different alignment procedures for the task at hand on a set of 185 protein pairs with similar structures but low-sequence similarity. Criteria based on the SCOP label detection and MaxSub scores are adopted to score the results. We investigate the efficacy of alignments based on sequence-sequence, sequence-profile, and profile-profile information. We confirm that with profile-profile alignments the results are better than with other procedures. In addition, we report, and this is novel, that the selection of the results of the profile-profile alignments can be improved by using Shannon entropy, indicating that this parameter is important to recognize good profile-profile alignments among a plethora of meaningless pairs. By this, we enhance the global search accuracy without losing sensitivity and filter out most of the erroneous alignments. We also show that when the entropy filtering is adopted, the quality of the resulting alignments is comparable to that computed for the target and template structures with CE, a structural alignment program.

Algorithms↗

PubMed2003

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.

MOTIVATION: A problem in predicting the topography of transmembrane proteins is the optimal localization of the transmembrane segments along the protein sequences, provided that each residue is associated with a propensity of being or not being included in the transmembrane protein region. From previous work it is known that post-processing of propensity signals with suited algorithms can greatly improve the quality and the accuracy of the predictions. In this paper we describe a general dynamic programming-like algorithm (MaxSubSeq, Maximal SubSequence) specifically designed to optimize the number and length of segments with constrained length in a given protein sequence. Previous application of our algorithm, has proved its effectiveness in the optimization task of both neural network and hidden Markov models output, and in this paper we present the detailed description of MaxSubSeq. RESULTS: We describe the application of MaxSubSeq to the location of both helical and beta strand transmembrane segments, optimizing the outputs derived with different predictive algorithms. For all-alpha transmembrane proteins we use both the standard Kyte-Doolittle (KD) hydropathy scale and the TMHMM predictor (http://www.cbs.dtu.dk/). Using a set of 188 well characterized membrane proteins, MaxSubSeq nearly doubles the correct location of transmembrane segments as compared to the standard KD hydrophobicity plot, reaching 51% accuracy. If MaxSubSeq is used to optimize the TMHMM method the accuracy increases from 68 to 72%. When used to regularize the prediction of beta transmembrane strands, obtained using both a neural network and a HMM based predictors, MaxSubSeq increases the accuracy per protein up to 72 and 73% respectively. AVAILABILITY: The program is available upon request to the authors, or it is accessible through our web server (http://gpcr.biocomp.unibo.it/predictors/)

Algorithms↗

PubMed1999

Rates and Equilibria of the Michael-Type Addition of Benzenethiol to 2-Cyclopenten-1-ones.

The triethylamine-catalyzed addition reactions of benzenethiol to 2-cyclopenten-1-one and its 2- and 3-methyl derivatives have been found to be appreciably reversible in chloroform solution. Rates and equilibria have been carefully measured at 25 degrees C in order to assess the negative influence on addition exerted by methyl groups substituted on the carbon-carbon double bond. 2-Methyl-2-cyclopenten-1-one has been found to react with benzenethiol under kinetic control to give the cis adduct as the sole detectable product in a highly stereoselective anti addition process. However, on prolonged reaction times the system slowly evolved toward a new state of equilibrium in which the more stable trans adduct, derived from a syn addition mode, was the predominant isomer.

Journal Article↗