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
Football through the eyes of a computer
14.06.2018 | Universität Konstanz
People recall information better through virtual reality, says new UMD study
14.06.2018 | University of Maryland
Moving into its fourth decade, AchemAsia is setting out for new horizons: The International Expo and Innovation Forum for Sustainable Chemical Production will take place from 21-23 May 2019 in Shanghai, China. With an updated event profile, the eleventh edition focusses on topics that are especially relevant for the Chinese process industry, putting a strong emphasis on sustainability and innovation.
Founded in 1989 as a spin-off of ACHEMA to cater to the needs of China’s then developing industry, AchemAsia has since grown into a platform where the latest...
The BMBF-funded OWICELLS project was successfully completed with a final presentation at the BMW plant in Munich. The presentation demonstrated a Li-Fi communication with a mobile robot, while the robot carried out usual production processes (welding, moving and testing parts) in a 5x5m² production cell. The robust, optical wireless transmission is based on spatial diversity; in other words, data is sent and received simultaneously by several LEDs and several photodiodes. The system can transmit data at more than 100 Mbit/s and five milliseconds latency.
Modern production technologies in the automobile industry must become more flexible in order to fulfil individual customer requirements.
An international team of scientists has discovered a new way to transfer image information through multimodal fibers with almost no distortion - even if the fiber is bent. The results of the study, to which scientist from the Leibniz-Institute of Photonic Technology Jena (Leibniz IPHT) contributed, were published on 6thJune in the highly-cited journal Physical Review Letters.
Endoscopes allow doctors to see into a patient’s body like through a keyhole. Typically, the images are transmitted via a bundle of several hundreds of optical...
Light detection and control lies at the heart of many modern device applications, such as smartphone cameras. Using graphene as a light-sensitive material for...
Water molecules exist in two different forms with almost identical physical properties. For the first time, researchers have succeeded in separating the two forms to show that they can exhibit different chemical reactivities. These results were reported by researchers from the University of Basel and their colleagues in Hamburg in the scientific journal Nature Communications.
From a chemical perspective, water is a molecule in which a single oxygen atom is linked to two hydrogen atoms. It is less well known that water exists in two...
13.06.2018 | Event News
08.06.2018 | Event News
05.06.2018 | Event News
18.06.2018 | Earth Sciences
18.06.2018 | Process Engineering
18.06.2018 | Life Sciences