Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

Selecting algorithms for Earth observation of climate within the European Space Agency Climate Change initiative: introduction to a special issue

This special issue is focused on the assessment of algorithms for the observation of Earth’s climate from environ- mental satellites. Climate data records derived by remote sensing are increasingly a key source of insight into the workings of and changes in Earth’s climate system. Producers of data sets must devote considerable effort and expertise to maximise the true climate signals in their products and minimise effects of data processing choices and changing sensors. A key choice is the selection of algorithm(s) for classification and/or retrieval of the climate variable. Within the European Space Agency Climate Change Initiative, science teams undertook systematic assessment of algorithms for a range of essential climate variables. The papers in the special issue report some of these exercises (for ocean colour, aerosol, ozone, greenhouse gases, clouds, soil moisture, sea surface temper- ature and glaciers). The contributions show that assessment exercises must be designed with care, considering issues such as the relative importance of different aspects of data quality (accuracy, precision, stability, sensitivity, coverage, etc.), the availability and degree of independence of validation data and the limitations of validation in characterising some important aspects of data (such as long-term stability or spatial coherence). As well as re- quiring a significant investment of expertise and effort, systematic comparisons are found to be highly valuable. They reveal the relative strengths and weaknesses of different algorithmic approaches under different observa- tional contexts, and help ensure that scientific conclusions drawn from climate data records are not influenced by observational artifacts, but are robust.

Transport and tourism : a weak symbiosis. An introduction to the special issue

“Tourism’s very existence depends on transport. Still, researchers in transportation and logistics do not show much interest in tourism whereas travel and tourism researchers pay more attention to accessibility than to transport.” These were the opening sentences of the call for papers for the TTRA European Chapter Conference “Transport and Tourism: Challenges, Issues and Conflicts” held in Rotterdam and Breda, The Netherlands from 22 to 24 April 2009.

Young peoples’ entrance to the workplace : Introduction to occupational health and safety

Negative outcomes of a poor work environment are more frequent among young workers. The aim of the current study was to study former pupils’ conditions concerning occupational health and safety by investigating the workplaces’, safety climate, the degree of implementation of SWEM and the their introduction programs. Four branches were included in the study: Industrial, Restaurant, Transport and Handicraft, specialising in wood. Semi-structured dialogues were undertaken with 15 employers at companies in which former pupils were employed. They also answered a questionnaire about SWEM. Former pupils and experienced employees were upon the same occasion asked to fill in a questionnaire about safety climate at the workplace. Workplace introduction programs varied and were strongly linked to company size. Most of the former pupils and experienced employees rated the safety climate at their company as high, or good. Employers in three of the branches rated the SWEM implemented at their workplaces to be effective. The Industry companies, which had the largest workplaces, gave the most systematic and workplace introduction for new employees. There are no results from this study explaining the fact that young workers have a higher risk for workplace accidents.

Introduction to Focus Issue: Statistical mechanics and billiard-type dynamical systems

Dynamical systems of the billiard type are of fundamental importance for the description of numerous phenomena observed in many different fields of research, including statistical mechanics, Hamiltonian dynamics, nonlinear physics, and many others. This Focus Issue presents the recent progress in this area with contributions from the mathematical as well as physical stand point. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4730155]

An introduction to numerical methods in low-dimensional quantum systems

This is an introductory course to the Lanczos Method and Density Matrix Renormalization Group Algorithms (DMRG), two among the leading numerical techniques applied in studies of low-dimensional quantum models. The idea of studying the models on clusters of a finite size in order to extract their physical properties is briefly discussed. The important role played by the model symmetries is also examined. Special emphasis is given to the DMRG.

From industrial economics to digital economics: an introduction to the transition

Includes bibliography

Introducción a la técnica de programación = Introduction to the technique of programming

Incluye Bibliografía