LoopIng: A template-based tool for predicting the structure of protein loops

MOTIVATION: Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function. RESULTS: We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop)

TiPs: A database of therapeutic targets in pathogens and associated tools

Motivation: The need for new drugs and new targets is particularly compelling in an era that is witnessing an alarming increase of drug resistance in human pathogens. The identification of new targets of known drugs is a promising approach, which has proven successful in several cases. Here, we describe a database that includes information on 5153 putative drug-target pairs for 150 human pathogens derived from available drug-target crystallographic complexes. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved.The need for new drugs and new targets is particularly compelling in an era that is witnessing an alarming increase of drug resistance in human pathogens. The identification of new targets of known drugs is a promising approach, which has proven successful in several cases. Here, we describe a database that includes information on 5153 putative drug-target pairs for 150 human pathogens derived from available drug-target crystallographic complexes

Improving the Security of Power Grids using Fuzzy Logic and Hidden Markov Models

The use of smart grid technology allows for bi-directional flow of electricity so that users can generate and sell energy back to the electric power grid. This advancing technology presents increased security vulnerabilities and risks. Various levels of vulnerability could be identified that are related to their causes and effects on the normal functioning of the power grid. In order to improve the security of power grids, fuzzy logic controllers were applied to circuits with different types of power converters. Hidden Markov analysis also proved helpful in increasing security. The results were analyzed and applied to smart grid technology models

PepComposer: computational design of peptides binding to a given protein surface

There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver

Local Dermonecrosis with Generalized Urticaria Probably Due to Loxosceles rufescens Bite

BACKGROUND: The spiders of the Loxosceles genus, commonly denoted as “brown spiders” or “Mediterranean recluse” or “brown recluse,” belong to the spider family Sicariidae, suborder Labidognatha, order Araneida, class Arachnida, and phylum Arthropoda. This spider is widespread in Africa and South/Central America, but it is also distributed in North America, in the West Indies, in the Mediterranean Europe, and in China. CASE REPORT: Here, we report the case of a severe dermonecrotic loxoscelism identified in Southern Italy, probably due to the bite of Loxosceles rufescens. The patient was a women admitted at hospital ER because of a little skin erythema that evolved toward a severe necrosis and ulceration within 20 days. After clinical and laboratory data excluded other local and systemic diseases, she was treated with a systemic and local therapy using corticosteroids and antibiotics with the diagnosis of loxoscelism. The healing from the local skin lesion occurred within 2 months, but the local pain, weakness, and discomfort lasted for a long time. CONCLUSION: It is the fisrt time that a possible case of systemic loxoscelism with skin generalized urticaria is reported in Italy

PIGSPro: prediction of immunoGlobulin structures v2

PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alignment for this portion of the molecule; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical structures are not available and the packing of the light and heavy chain if derived from different templates. Each of these steps has been improved including updated methods developed along the years. Last but not least, the user interface has been completely redesigned and an automatic monthly update of the underlying database has been implemented. The method is available as a web server at http://biocomputing.it/pigspro

Fully Enclosed Microfluidic Paper-Based Analytical Devices

This article introduces fully enclosed microfluidic paper-based analytical devices (microPADs) fabricated by printing toner on the top and bottom of the devices using a laser printer. Enclosing paper-based microfluidic channels protects the channels from contamination, contains and protects reagents stored on the device, contains fluids within the channels so that microPADs can be handled and operated more easily, and reduces evaporation of solutions from the channels. These benefits extend the capabilities of microPADs for applications as low-cost point-of-care diagnostic devices

Correction to Fully Enclosed Microfluidic Paper-Based Analytical Devices

There is an error in the units of the concentrations of potassium iodide and trehalose described in the experimental details on page 1581. The correct concentrations are 0.6 M potassium iodide and 0.3 M trehalose

Evaluation and Management of Patients with Methomyl Poisoning – A Case Report

The Apulian Poison Centre (PC) of Foggia, Italy, annually manages numerous consultations concerning certain or suspected poisonings from pesticides, starting at the same time a careful activity related to the risk assessment phase. The management of the exposure to pesticides and to other chemicals, and the alerting of the “National center for chemicals, cosmetics and consumer protection” at the Istituto Superiore di Sanità (ISS), actively contributes to the improvement of products quality and safety. Thus, leading to a reduction in the number of intoxications - and therefore of the accesses to the emergency services - allows greater protection for workers, bystanders, residents and consumers. The reported case of methomyl poisoning has been of fundamental importance both from the medical point of view and for the management of the intoxicated patient, both for the risk assessment actions, and for cooperation with the competent authorities, generating discussion points on the regulations in force between PCs and National Competent Authority. It follows that the feedback of intoxication in an emergency can lead to improvements in the management and risk mitigation measures in order to reach a greater protection of human, animal, and environmental health. In addition, the regulatory feedback deriving from these reports is an input to the increase product quality improvement (mixtures, labels, packaging, and risk communication) leading to a greater protection of potential exposed subjects. The importance of creating an information and management network that allows the optimization of the flow of information deriving from PCs arises. The actions taken are therefore described, both relating to the management of the emergency, and relating to the subsequent information flow and to the measures for containing the consequent risks