A5022624631- Mass Spectrometry Techniques and Applications
- Protein Structure and Dynamics
- Scientific Computing and Data Management
- Receptor Mechanisms and Signaling
- Network Security and Intrusion Detection
- Advanced Malware Detection Techniques
- Machine Learning in Materials Science
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Neuropeptides and Animal Physiology
- Dark Matter and Cosmic Phenomena
- Distributed and Parallel Computing Systems
- Microfluidic and Capillary Electrophoresis Applications
- Research Data Management Practices
- Digital Radiography and Breast Imaging
- Analytical Chemistry and Sensors
- Acoustic Wave Resonator Technologies
- Protein Kinase Regulation and GTPase Signaling
- Pharmacological Effects and Assays
- Bioinformatics and Genomic Networks
- Chemical Synthesis and Analysis
- Genomics and Rare Diseases
- Machine Learning in Bioinformatics
Leipzig University
2017-2025
University of Copenhagen
2020-2024
Stockholm University
2023-2024
KTH Royal Institute of Technology
2023-2024
Novozymes (Denmark)
2023-2024
Science for Life Laboratory
2024
Tsinghua University
2023
Institute of Biophysics
2023
Stanford Medicine
2023
Laboratoire de Biochimie Théorique
2023
The crystal structure of the β2-adrenergic receptor (β2AR) bound to G protein adenylyl cyclase stimulatory (Gs) captured complex in a nucleotide-free state (β2AR-Gsempty). Unfortunately, β2AR-Gsempty does not provide clear explanation for coupling specificity. Evidence from several sources suggests existence transient between β2AR and GDP-bound Gs (β2AR-GsGDP) that may represent an intermediate on way formation contribute Here we present with carboxyl terminal 14 amino acids Gαs along...
G protein-coupled receptors (GPCRs) constitute a functionally diverse protein family and are targets for broad spectrum of pharmaceuticals. Technological progress in X-ray crystallography cryogenic electron microscopy has enabled extensive, high-resolution structural characterisation GPCRs different conformational states. However, as highly dynamic events underlie GPCR signalling, complete understanding functionality requires insights into their dynamics. Here, we present large dataset...
The possible effects of mutations on stability and function a protein can only be understood in the context 3D structure. MutationExplorer webserver maps sequence changes onto structures allows users to study variation by inputting changes. As user enters variants, model evolves, estimated energy are highlighted. In addition basic per-residue input format, also upload an entire replacement sequence. Previously purview desktop applications, such back-mutate PDB wildtype single step. Another...
Given the need for modern researchers to produce open, reproducible scientific output, lack of standards and best practices sharing data workflows used analyze molecular dynamics (MD) simulations has become an important issue in field. There are now multiple well-established packages perform simulations, often highly tuned exploiting specific classes hardware, each with strong communities surrounding them, but very limited interoperability/transferability options. Thus, choice software...
The rise of open science and the absence a global dedicated data repository for molecular dynamics (MD) simulations has led to accumulation MD files in generalist repositories, constituting dark matter — that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found indexed about 250,000 2000 datasets from Zenodo, Figshare Open Science Framework. With focus on produced by Gromacs software, illustrate potential offered...
G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data GPCRs sparse yet important for elucidating the molecular basis GPCR-related diseases performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The...
Internal water molecules play an essential role in the structure and function of membrane proteins including G protein-coupled receptors (GPCRs). However, technical limitations severely influence number certainty observed 3D structures. This may compromise accuracy further structural studies such as docking calculations or molecular dynamics simulations. Here we present HomolWat, a web application for incorporating into GPCR structures by using template-based modelling homologous obtained...
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and computational environments. Here we show how applications can be created a reproducible manner when simple design goals for reproducibility met. We describe implementation test server framework 40 benchmarks, covering numerous Rosetta...
Abstract Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv tool that streams MD trajectories displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration collaborative visual analysis. We have now enhanced to further simplify upload sharing improve their online viewing With new instance, simplifies creation sessions, which allows...
SuperLooper2 (SL2) (http://proteinformatics.charite.de/sl2) is the updated version of our previous web-server SuperLooper, a fragment based tool for prediction and interactive placement loop structures into globular helical membrane proteins. In comparison to version, SL2 benefits from both considerably enlarged database fragments derived high-resolution 3D protein proteins, integration new viewer. The database, now with double content, significantly improved coverage conformations quality....
G protein-coupled receptors (GPCRs) are intensively studied due to their therapeutic potential as drug targets. Members of this large family transmembrane receptor proteins mediate signal transduction in diverse cell types and play key roles human physiology health. In 2013 the research consortium GLISTEN (COST Action CM1207) was founded with goal harnessing substantial growth knowledge GPCR structure dynamics push forward development molecular modulators function. The success GLISTEN,...
The rise of open science and the absence a global dedicated data repository for molecular dynamics (MD) simulations has led to accumulation MD files in generalist repositories, constituting dark matter — that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found indexed about 250,000 2000 datasets from Zenodo, Figshare Open Science Framework. With focus on produced by Gromacs software, illustrate potential offered...
A bstract The possible effects of mutations on stability and function a protein can only be understood in the context 3D structure. M utation E xplorer webserver maps sequence changes onto structures allows users to study variation by inputting changes. As user enters variants, model evolves, estimated energy are highlighted. In addition basic per-residue input format, also upload an entire replacement sequence. Previously purview desktop applications, such back-mutate PDB wildtype single...
The rise of open science and the absence a global dedicated data repository for molecular dynamics (MD) simulations has led to accumulation MD files in generalist repositories, constituting
The rise of open science and the absence a global dedicated data repository for molecular dynamics (MD) simulations has led to accumulation MD files in generalist repositories, constituting dark matter — that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found indexed about 250,000 2,000 datasets from Zenodo, Figshare Open Science Framework. With focus on produced by Gromacs software, illustrate potential offered...
The rise of open science and the absence a global dedicated data repository for molecular dynamics (MD) simulations has led to accumulation MD files in generalist repositories, constituting dark matter - that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found indexed about 250,000 2,000 datasets from Zenodo, Figshare Open Science Framework. With focus on produced by Gromacs software, illustrate potential offered...
Abstract G protein-coupled receptors (GPCRs) are involved in numerous physiological processes and the most frequent targets of approved drugs. The explosion number new 3D molecular structures GPCRs (3D-GPCRome) during last decade has greatly advanced mechanistic understanding drug design opportunities for this protein family. While experimentally-resolved undoubtedly provide valuable snapshots specific GPCR conformational states, they give only limited information on their flexibility...
Abstract Next-generation sequencing of human genomes reveals millions missense variants, some which may lead to loss protein function and ultimately disease. We here investigate variants in membrane proteins — key drivers cell signaling recognition. find enrichment pathogenic the transmembrane region across 19,000 functionally classified proteins. To accurately predict variant consequences, one fundamentally needs understand reasons for pathogenicity. A mechanism underlying pathogenicity...
Voronoia4RNA (http://proteinformatics.charite.de/voronoia4rna/) is a structural database storing precalculated atomic volumes, packing densities (PDs) and coordinates of internal cavities for currently 1869 RNAs RNA–protein complexes. Atomic PDs are measure van der Waals interactions. Regions low PD, containing water-sized cavities, refer to local structure flexibility or compressibility. RNA molecules build up the skeleton large molecular machineries such as ribosomes form smaller flexible...