Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design, and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.

MOTIVATION: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. RESULTS: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. AVAILABILITY AND IMPLEMENTATION: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.

The simulation plays an important role in biomedical image analysis as it can inherently provide large collections of image data with absolute ground truth. Compared to real image data typically annotated by some expert, the computer generated data still lacks the authenticity due to the simplifications of various natural phenomena. In this paper, we focus on simulating the photobleaching effect and the uneven illumination, being simplified or even omitted from the majority of present simulation toolkits, to considerably improve the authenticity of computer generated data.

Networking infrastructure is a vital part of virtual computer clusters. This paper describes VirtCloud, a system for interconnecting virtual clusters in a state-wide network based on advanced features available in academic networks. The system supports dynamic creation of virtual clusters without the need of run-time administrative privileges on the backbone core network, encapsulation of the clusters, controlled access to external sources for cluster hosts, full user access to the clusters, and optional publishing of the clusters. The paper describes architecture of the system, and prototype implementation in MetaCenter (Czech national Grid infrastructure) using Czech national research network CESNET2. Feasibility of the concept is evaluated through a series of measurements demonstrating that the network performance of the system is satisfactory.

Interactions between large biomolecules and smaller bio-active ligands are usually studied through a process called docking. Its aim is to find an energetically favorable orientation of a ligand within an active site of abiomolecule. Chemical reactions take place in active siteand the role of the ligand is either to speed up, slow down or change the reaction (e.g., an enzyme catalyzed hydrolysis), which is why it can have huge pharmaceutical or other commercial impact. We present a tool that supports effective management and control of a typical workflow of docking parametric study. Selected subsets of ligands and protein trajectory snapshots can be displayed in three different views and further analyzed. Finally, the application supports spawning and steering underlying computations running on the Grid.

Abstract Job Provenance (JP), part of the gLite Grid middleware, is a service that keeps long‐term trace on completed computations for further reference. It is a job‐centric service, keeping records about job life cycle, its environment, inputs/outputs, user parameters, and annotations. During the first provenance challenge, we explored the relation between a specific job‐centric Grid‐oriented provenance and a more general data provenance approach. The challenge represents a use case which emphasizes fields that were not priorities in the original JP design. However, we proved that the design is sufficiently general to cope with this mode of use. We also identified several areas where it is feasible to extend the current implementation. Copyright © 2007 John Wiley & Sons, Ltd.

Current collaborative tools are often not able to profit from existing systems for user management. It is therefore necessary for collaborative systems to administrate their users using their own solutions, which may not be adequate in terms of scalability or security. Many users may also experience problems working with authentication credentials (e.g. digital certificates) employed by collaborative systems. In this paper, we propose a general framework to provide easy-to-use yet secure access to collaborative systems, which offers a general middleware layer to accommodate various types of collaborative tools. The framework utilizes the emerging model of federations, which allows to provide a user-friendly means of logging in to a collaborative system as well as a solid basis for specifying access control policies. The framework handles all security aspects in a transparent way without requiring the users to perform complicated tasks. Using user attributes maintained in the federation, it is also possible to implement efficient and dynamic group management of the collaborating users.

The Testbed and Applications working group of the European Grid Forum (EGrid) is actively building and experimenting with a grid infrastructure connecting several research-based supercomputing sites located in Europe. The paper reports on our first feasibility study: running a self-migrating version of the Cactus simulation code across the European grid testbed, including "live" remote data visualization and steering from different demonstration booths at Supercomputing 2000, in Dallas, TX. We report on the problems that had to be resolved for this endeavour and identify open research challenges for building production-grade grid environments.