Protein dynamics | NMR-based proteomics data analysis
Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for the analysis of molecule dynamics.
Allows to study molecular dynamics by analyzing nuclear magnetic resonance (NMR) relaxation data. Relax has been written as a modular collection of data analysis tools. A Graphical User Interface (GUI), developed for model-free analysis, is integrated into the software package. The program supports several analysis such as Model-free analysis, Nuclear overhauser effect (NOE) or Reduced Spectral Density Mapping (RDSM). It can also create the input files for both Modelfree and Dasha, execute both programs in-line, and then read their output.
Performs general ensemble-based validation step and a simple and straightforward, multi-purpose selection option. CoNSEnsX permits to assess the correspondence of ensembles to experimental nuclear magnetic resonance (NMR) parameters. It can be used for protein structure prediction, ensemble-based evaluation of protein models is an important issue in assessing the accuracy of the predicted conformations. The tool will aid the choice of suitable low-dimensional projections.
Predicts absolute per-residue fluctuation from a three-dimensional protein structure. FlexPred is designed to predict the fluctuations exhibited by a protein during a 10 ns MD simulation. It uses static features of a protein structure to predict MD residue fluctuation in 3D. Its predictions were evaluated using Pearson’s correlation coefficient. This tool is presented under two versions: a stand-alone and a web server.
Analyzes Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion profiles. ShereKhan provides an easy way to calculate exchange parameters (rates, relative populations and their structural information) of molecules. The workflow has been designed to guide user through the process from uploading data to the calculation of the exchange rates and populations of the states. User uploaded data are stored temporary on the server and deleted when leaving the application.