Dynamics Center

Highlights

Comprehensive

Dynamics Center is the only commercial software for advanced analysis methods for relaxation, diffusion, kinetics, and protein dynamics

Flexible

Multiple, parallel analysis of any types of spectra

Dynamics Center is a unique comprehensive software solution for relaxation, diffusion, and kinetics analyses. It offers a rich collection of methods especially in protein and nucleotide applications. The analysis of NMR data containing one or two non-frequency dimensions is performed automated or semi-automated.

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Features

Diverse collection of advanced methods, especially in protein and nucleotide applications
Multiple, parallel analysis of any type of spectra: series of 1Ds / 2Ds / 3Ds, pseudo 2Ds, pseudo 3Ds and time domain data
Unified workflow for all kinds of relaxation, diffusion, and kinetics analyses
Automatic data fitting and best model selection
Library of predefined fitting functions. User defined fitting functions optional
Powerful algorithm for Inverse Laplace Transformation
Unique interactive multi spectra display features

Benefits

Low learning efforts needed: All methods are following the same workflow with the same general components
User input is minimized if experiments are performed with Bruker pulse programs
Highly efficient: multiple parallel execution of different methods
Ensured data quality: Advanced display features enable interactive inspection of the data integrity in the light of analytical results
Flexible: Data can be imported and exported in different formats as Excel, tab separated text files, or pdf

Applications

General Dynamics

General methods perform fast and offer data analysis for any molecule or mixture. This includes automated optimization of acquisition parameters, e.g., for T1 and T2 experiments.

Relaxation (T1, T2, T1rho)
Diffusion & Kinetics
Solid states (REDOR, CP)
Special methods (Arrhenius, 2D Laplace)

The analysis is based on peak integrals, is optimized in speed and flexibility, allows multi-component modelling, has many built-in functions and allows user defined functions.

One can set all parameters from external programs at runtime and integrate them into various automation environments. Routine analysis can also be triggered via TopSpin.

Protein Dynamics

The protein dynamics toolset is a collection of methods to determine protein dynamics from relaxation parameters, motional order parameters, directional dynamics via exact distance determination.

Successful methods of biological NMR-spectroscopy are implemented based on liquid-state as well as solid-state NMR. Data are used as series of 2D, pseudo 3D or 3D spectra.

Further special methods include REX, CEST,
TRACT and protein-ligand binding
Special result display on structures (PDB) and
protein sequences (FASTA)
Advanced display tools for checking of results
and experimental data
Multiple import options for assignments (peaklists
or shiftlists) from scientific programs like CCPNMR,
Sparky and others
Multiple export options for structure calculation with CYANA, XPLOR, ARIA

Time Domain Dynamics

Time Domain Dynamics is a new tool for the extraction of relaxation information from NMR time domain data recorded with Bruker’s benchtop MiniSpec. Special methods are available additionally:

FormCheck to quantify components in solid mixtures
2D Inverse Laplace to study material properties
TD RheoNMR to combine NMR and Rheometry

The software is ideally suited for routine applications, optimization of experiments and additionally provides the infrastructure for automated analysis of large sample batches.

Diffusion in Action on a Benzine Sample

Diffusion experiments are routinely performed, e.g., to check for components in mixtures. Advanced curve fitting and inverse Laplace transform (ILT) are used to reveal details. Multi visualization tools (e.g., double log scale, residual display, amplitude profile display) provide insight into the quality. Quick overview is obtained via DOSY plots either based on fit results or ILT.

Get Details wherever needed

Context sensitive properties provide interesting information, e.g., which model function was used and which results and error have been obtained, how different are experimental and back calculated data, do the residuals possibly indicate a systematic error?

Report and Export

PDF reporting which includes graphics and result tables can be used to document work. Users interested in more details, e.g., all peak integrals which have been used may prefer export to EXCEL or text. This allows recalculation with other software or creating alternative graphical results displays.

NMR Helps to Follow Kinetics Reactions on Atomic Level

Available with series of 1D and 2D experiments. In the example all 2D spectra are stacked into 3D cube. With a slider you can navigate to any spectrum and select any peak with the cursor. The corresponding intensity profile is shown online. Cumulated curve display shows the overall reaction.

Investigating Anisotropic Properties of Materials

Different combinations of 2D diffusion-diffusion, diffusion-relaxation or relaxation-relaxation experiments are performed. From the 2D distributions of the respective parameters as obtained by 2D inverse Laplace transform information is obtained about content and anisotropy.

Determination of Rotational Correlation Times

This value is needed in many calculations and can for example be estimated from the molecular weight. The TRACT method determines it directly from ratios of 15N longitudinal and transverse cross-correlated relaxation rates from the coordinated rotation of two nuclei in a magnetic field. Only a large signal area needs to be defined.

Dipolar Order Parameters Reveal Protein Backbone Dynamics

REDOR buildup curves are modelled with a series of Bessel functions to get dipolar couplings. Order parameters are derived from these and shown as a histogram on the amino acid sequence as well as a colored cartoon. Rigid and flexible regions of the molecule get visible.

Determination of Distances in Large Molecules

The exact NOE method is implemented. Buildup curves are modelled to obtain cross relaxation rates and distances. The distances are then corrected for spin diffusion assuming an initial structure exists. Agreement with the structure is seen in correlation plots. Restraints files are generated for ARIA, CNS and CYANA to obtain better structure.

Get dynamic Parameters of Protein Backbones

HetNoe, T1 and T2 experiments need to be combined and used for different model calculations. Information obtained ranges from spectral densities, relaxation exchange, correlation times to order parameters. Isotropic modelling can always be performed, anisotropic modelling is available if the protein structure is supplied. Data obtained at different magnetic field strengths can be incorporated into one calculation.

An Exciting Combination: NMR and Rheology, TDRheoNMR

While NMR delivers dynamic information, rheology is used to measure mechanical properties such as viscosity. The example shows two cocoa butter crystallization experiments, where in the upper run the Rheo-NMR MiniSpec accessory applied a shear field up to the point where the sample rapidly solidifies. In the lower graph, no shear is applied at otherwise identical conditions, leading to a substantially slower and later solidification. The upper graph additionally displays the imported rheological data (viscosity). Such experiments can be used to optimize the composition of samples and perform quality control.

Specifications

Client/Server architecture for any programming environment
Is also included into other products like InsightMR, and FormCheck
Automated interaction with other software such as IconNMR, BioTop
Available on Windows, Linux and Mac

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