A key research issue is the study of individual residues, the building blocks of proteins, and their interactions in the 3D protein structure. Scientists at the Max Planck Institute for Informatics, Saarbruecken, Germany, developed innovative software for the detailed analysis and visualization of residue interactions in protein structures.
To date, the 3D structures of several 10,000 proteins have been determined experimentally. The structures are usually visualized and analyzed in 3D viewers to understand protein function on the molecular level. However, the visual complexity of protein structures renders it difficult to focus on individual residues and their long-range molecular interactions.
Researchers at the Max Planck Institute for Informatics now offer the new software tools RINalyzer and RINerator (http://www.rinalyzer.de) that support the automated generation, visualization, and interactive analysis of residue interaction networks (RINs). A RIN is derived from the corresponding 3D protein structure and consists of network nodes and connecting edge lines that represent protein residues and their interactions, respectively. Recent studies have shown that RINs are especially useful for identifying functionally important residues and characterizing their impact on protein structure and function.
"We already applied RINs successfully to characterize the functional effect of residue changes that are located far away from the drug-binding site in protein structures. In the past, we had to perform the analysis and the visualization manually because no such tool as RINalyzer was available," explains Francisco S. Domingues, who has recently moved from the Max Planck Institute to EURAC research in Bolzano, Italy.
RINalyzer is the first tool that combines the 3D structure view of a protein with its network representation. Protein residues selected in a RIN are automatically highlighted in the 3D protein structure, and vice versa. "To investigate complex protein-structure relationships, we provide molecular biologists with free, user-friendly software. The rich versatility of RINalyzer does not require previous network analysis expertise or programming knowledge from the users," says Nadezhda T. Doncheva, research scientist at the Max Planck Institute.
RINalyzer is complemented by the large online database RINdata that contains over 50,000 precomputed RINs for most protein structures in the publicly available Protein Data Bank. "Our novel tools have the great potential to become a standard application for biologists alongside other existing approaches to protein structure visualization," notes Mario Albrecht, research group leader at the Max Planck Institute in the local Cluster of Excellence on Multimodal Computing and Interaction.
Bertram Somieski | Max-Planck-Institut
Next Generation Cryptography
20.03.2018 | Fraunhofer-Institut für Sichere Informationstechnologie SIT
TIB’s Visual Analytics Research Group to develop methods for person detection and visualisation
19.03.2018 | Technische Informationsbibliothek (TIB)
Satellites in near-Earth orbit are at risk due to the steady increase in space debris. But their mission in the areas of telecommunications, navigation or weather forecasts is essential for society. Fraunhofer FHR therefore develops radar-based systems which allow the detection, tracking and cataloging of even the smallest particles of debris. Satellite operators who have access to our data are in a better position to plan evasive maneuvers and prevent destructive collisions. From April, 25-29 2018, Fraunhofer FHR and its partners will exhibit the complementary radar systems TIRA and GESTRA as well as the latest radar techniques for space observation across three stands at the ILA Berlin.
The "traffic situation" in space is very tense: the Earth is currently being orbited not only by countless satellites but also by a large volume of space...
An international team of researchers has discovered a new anti-cancer protein. The protein, called LHPP, prevents the uncontrolled proliferation of cancer cells in the liver. The researchers led by Prof. Michael N. Hall from the Biozentrum, University of Basel, report in “Nature” that LHPP can also serve as a biomarker for the diagnosis and prognosis of liver cancer.
The incidence of liver cancer, also known as hepatocellular carcinoma, is steadily increasing. In the last twenty years, the number of cases has almost doubled...
In just a few weeks from now, the Chinese space station Tiangong-1 will re-enter the Earth's atmosphere where it will to a large extent burn up. It is possible that some debris will reach the Earth's surface. Tiangong-1 is orbiting the Earth uncontrolled at a speed of approx. 29,000 km/h.Currently the prognosis relating to the time of impact currently lies within a window of several days. The scientists at Fraunhofer FHR have already been monitoring Tiangong-1 for a number of weeks with their TIRA system, one of the most powerful space observation radars in the world, with a view to supporting the German Space Situational Awareness Center and the ESA with their re-entry forecasts.
Following the loss of radio contact with Tiangong-1 in 2016 and due to the low orbital height, it is now inevitable that the Chinese space station will...
Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP, provider of research and development services for OLED lighting solutions, announces the founding of the “OLED Licht Forum” and presents latest OLED design and lighting solutions during light+building, from March 18th – 23rd, 2018 in Frankfurt a.M./Germany, at booth no. F91 in Hall 4.0.
They are united in their passion for OLED (organic light emitting diodes) lighting with all of its unique facets and application possibilities. Thus experts in...
A new scenario seeking to explain how Mars' putative oceans came and went over the last 4 billion years implies that the oceans formed several hundred million...
23.03.2018 | Event News
19.03.2018 | Event News
16.03.2018 | Event News
23.03.2018 | Life Sciences
23.03.2018 | Materials Sciences
23.03.2018 | Process Engineering