NMR Software & Simulations

Students in ‘Principles of Magnetic Resonance’ (PMR) at ASU in Spring 2020 need to register on Spintropy (www.spintropy.com) and Bruker (www.bruker.com) for academic accounts.  Spintropy is a cloud service (developed by Dr. Samrat Amin) for NMR data and Bruker has a freely available software package (free for ACADEMIC users/students), TopSpin, that will be needed for data processing and analysis.   A tutorial for Spintropy registration and Bruker Topspin installation are provided below:

• Spintropy Registration Tutorial. Spintropy_Account_Setup_PMR_Class.pdf
  • IF YOU HAVE A SPINTROPY RESEARCH ACCOUNT, please use a different email to register for a PMR Spring 2020 class Spintropy account (for billing purposes).
• Bruker Topspin Software (Windows, Mac, Linux)
  • Register as an academic user (student) with Bruker.
  • Download and install Topspin on your computer. (Std or Iso images)
  • Reference Bruker Topspin NMR Software Manuals and Operator’s Guides.
  • Use the Bruker Topspin Example Data and familiarize yourself with basic 1H data processing, data analysis, and plotting (making a suitable figure).

Links to NMR Software, Applications & Analysis

• Bruker NMR Software Portfolio.
• OpenVnmrJ – Open Source parts of VnmrJ 4.2, used for NMR Data processing and acquisition.
• ssNAKE – A spectra fitting and processing standalone program designed primarily for solids NMR. A stand alone GUI installer is provided as well as python source code on a git.
• NMRFx -Integrated Software for NMR Analysis
  • Norris, M., Fetler, B., Marchant, J., & Johnson, BA., (2016) J. Biomol. NMR 65:205-216. NMRFx Processor: a cross-platform NMR data processing program
• NMR Glue – A module for working with NMR data in Python, providing a robust environment for rapidly developing new methods for processing, analyzing, and visualizing NMR data. Nmrglue also provides a framework for connecting existing NMR software packages, including Agilent/Varian, Bruker, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit.
• Delta NMR – Jeol
• MetreLab Research – Mnova.
• Chenomx – NMR Metabolomics.
• RMN – Grandinetti Group – Software – Now part of PhySy Calc.
• MatNMR – Provides a MATLAB interface for process, analyze and visualize 1D and 2D nuclear magnetic resonance (NMR) data.
• rNMR – visualizing and interpreting one and two dimensional NMR data.
• Perch Solutions.
• NMRbox – is a resource for biomolecular NMR (Nuclear Magnetic Resonance) software. It provides tools for finding the software you need, documentation and tutorials for getting the most out of the software, and cloud-based virtual machines for executing the software.
• NMR information Server: Software.
• NMR Wiki– NMR Software Wiki.
• gNMR – Unsupported package.
• DMFit 2015 – A spectra fitting standalone program especially well-suited for fitting amorphous solids.
• MagresView – An intuitive opensource tool for visualization of ab-inito predicted parameters.
• CCPN – The Collaborative Computing Project for NMR (CCPN) aims to bring together computational aspects of the scientific community involved in NMR spectroscopy.

Links to MRI Software, Processing and Visualization

• ParaVision360 – Bruker MRI Software.
• ImageJ Plugin.
• MR Research Center – MRRC: Sofware Resources.
• MRIlab: A MATLAB Numerical Simulation Platform for Magnetic Resonance Imaging (MRI)
• SIMRI: a versatile and interactive Magnetic Resonance Imaging (MRI) simulator.
• MIPAV -The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy.
• FreeSurfer – An open source software suite for processing and analyzing (human) brain MRI images.
• MicroDicom – MicroDicom is application for primary processing and preservation of medical images in DICOM format.
• BrianSuite – A collection of open source software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain.
• OsiriX – A widely used DICOM viewer.

Links to Simulation and Computation Software and Programs

• NMRSIM – NMR Simulations within Bruker’s TopSpin software. (v. 2.8 pdf manual)
  • Its confusion but there is also a nmrsim python library for liquids NMR.
• SpinEvolution – highly efficient computer program for the numerical simulation of NMR experiments and general spin dynamics.
  • M.Veshtort, R.G.Griffin, SPINEVOLUTION: A powerful tool for the simulation of solid and liquid state NMR experiments, J. Magn. Reson., 178 (2006) 248-282.
• NMR Groups at Aarhus Univ. – Software
  • VirtualSpectrum – Tool for simulating peak lists for multi-dimensional NMR spectra.
  • jsNMR – jsNMR is a JavaScript-based spectrum viewer.
  • SIMMOLvmd– scripts for VMD.
  • Simpson– SimMol, Asics: Solid-State NMR experiment simulation.
• Pygamma – GAMMA is a C++ library for the simulation of magnetic resonance (NMR, MRS) experiments.
• NMRdb.org – Tools for NMR spectroscopists
  • Prediction of 1H NMR coupling constants with associative neural networks trained for chemical shifts J. Chem. Inf. Model. 2007, 47/(6), 2089-2097.
  • Banfi, D.; Patiny, L. www.nmrdb.org: Resurrecting and processing NMR spectra on-line Chimia, 2008, 62(4), 280-281.
  • Andrés M. Castillo, Luc Patiny and Julien Wist. Fast and Accurate Algorithm for the Simulation of NMR spectra of Large Spin Systems. Journal of Magnetic Resonance 2011.
  • Aires-de-Sousa, M. Hemmer, J. Gasteiger, “ Prediction of 1H NMR Chemical Shifts Using Neural Networks”, Analytical Chemistry, 2002, 74(1), 80-90.
  • 1H NMR prediction: https://www.nmrdb.org/service.php?name=nmr-1h-prediction&smiles=c1ccccc1CC
  • 13C NMR prediction: https://www.nmrdb.org/service.php?name=nmr-13c-prediction&smiles=c1ccccc1CC
  • COSY prediction: https://www.nmrdb.org/service.php?name=cosy-prediction&smiles=c1ccccc1CC
  • HSQC/HMBC prediction: https://www.nmrdb.org/service.php?name=hmbc-prediction&smiles=c1ccccc1CC
  • All predictions: https://www.nmrdb.org/service.php?name=all-predictions&smiles=c1ccccc1CC
• ChemInfo – Chemistry Tools, similar/same NMR as NMRdb.org
  • NMR Prediction
• ChemDoodle – Simulate NMR
• WinDnmr-Pro– Windows program for simulating NMR spectra.
• NMR Predict – MestreLab Research, Mnova, Software.
• ACD/NMR Predictors– NMR Predictor Software.
• Orange NMR App – NMR Spectra Prediction.
  • The prediction algorithm is derived on: K. A. Blinov, E. D. Smurnyy, T. S. Churanova, M. E. Elyashberg, A. J. Williams, Chemom. Intell. Lab. Syst. 2009, 97, 91
• SpinDynamics.org –Spinach, SpinXML.
• NMRShiftdb – NMRshiftdb2.
  • Rapid prediction of NMR spectral properties with quantified uncertainty, J. ChemInfomatics (2019).
• NMR Simulation – Simulate NMR spectra from spin systems: GitHub.

BioMolecular

• NMRPipe – UNIX-based collection of programs and scripts for manipulating multidimensional Nuclear Magnetic Resonance (NMR) data
• YASARA – NMRStructure Determination – Protein.
• Glycan NMR Tools
• NmrLineGuru: NMR Binding.
  • Feng, C., Kovrigin, E.L. & Post, C.B. NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models. Sci Rep 9, 16023 (2019). https://doi.org/10.1038/s41598-019-52451-8
• Sparky – NMR Assignment and Integration Software
• SPINS – Standarzing Protein NMR Storage.
• CCPN – The Collaborative Computing Project for NMR (CCPN) is a project that aims to bring together computational aspects of the scientific community involved in NMR spectroscopy of biological molecules, especially those who work in the field of protein NMR.