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On-line Tools | Data Bank | Resources | Education | Company | Institute | Software
On-line Tools
  • NMRtist - NMRtist is a cloud computing service for the fully automated analysis of protein NMR spectra (e.g. peak picking, chemical shift assignment, structure determination) using deep learning-based approaches. Each project created in NMRtist receives 30 GB of private storage, which can be filled by experimental data and analyzed using the available applications. You don't need to have any hardware resources or follow complex software configuration processes. NMRtist applications can be executed by just few mouse clicks in your web browser. All calculations are executed on NMRtist computational nodes, making the results available for download from NMRtist website.
  • I-PINE - I-PINE accepts, as input, the sequence of the protein plus peak lists (or spin systems) from a variety of NMR experiments and offers automated backbone and sidechain assignments, detection and automated correction of potential referencing problems or inconsistent assignments, secondary structure determination, 3D structure prediction, cysteine oxidation, proline isomerization and hydrophobic core detection.
  • ncIDP- Neighbor Corrected IDP Library - Allows prediction of nuclear shielding constants for a polypeptide sequence. ncIDP is a web application consisting of 3 reversible steps. The software can be interfaced with available protein chemical shift analysis tools, such as chemical shift index (CSI), structural propensity score assessment for intrinsically disordered proteins, and protein structure modeling from chemical shift information (CS-Rosetta).
  • RCI- Random Coil Index - RCI webserver predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (Cα, CO, Cβ, N, Hα, NH) and estimating values of model-free order parameters as well as per-residue RMSF of NMR and MD ensembles from the Random Coil Index.
  • ShereKhan- Calculating molecular exchange rates - Define your experimental data in this section. More then one file can be uploaded, each file representing data measured at different magnetic field. If data were measured at multiple field strengths, the residue types and numbers will be compared and chemical shift differences fitted globally to calculate kinetic parameters.
  • ExPASy-Bioinformatics Resource Portal - ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu).
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Data Bank
  • BioMagResBank - A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids [BMRB]
  • Protein Data Bank - The protein Data Bank is operated by the Research collaboratory for Structural Bioinformatics (RCSB) [PDB]
Resources
  • BioTRec - NMR Core - National Biotechnology Research Park (NBRP) NMR Core Facility is one of the supporting core facility of 「Medicinal Chemistry and Analytical Core Facilities」. Together with the Mass Spectrometry Core Facility and Medicinal Chemistry Core Facility, we aims to support pharmaceutical-related research and development, especially for biomedical technology industry to develop small molecule drugs. Our technical and research staffs can provide professional consulting and analysis services to boost the quality and quantity of drug research and development in the biotechnology industry. In the near future, we will collaborate with the NBRP Animal Imaging Facility and Academia Sinica High Field Nuclear Magnetic Resonance Center to provide one-stop service and consultation on small molecule synthesis and analysis, macromolecular structure analysis and animal imaging for biotech companies and other R&D groups.
  • NMR Knowledge Base - This web site is dedicated to bring you the most complete NMR resource site available on the Internet
  • NMR Spectroscopy at EMBL??- This NMR WWW Server contains Serrano, Sattle, and Nilges's groups and lots of EMBL NMR Links
  • National Magnetic Resonance Facility At Madison (NMRFAM) - This is an NIH-supported biomedical Technology Research Resource Center at University of Wisconsin- Madison
Education
Company
  • BRUKER - Bruker's NMR Division in USA
  • BRUKER -Bruker's NMR Division in Germany
Institute
Software
  • Molmol - MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.
  • InsightII - 3D graphical environment for molecular modeling
  • CNS- Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
  • XPLOR-NIH - XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH.
  • TopSpin- For NMR data analysis and the acquisition and processing of NMR spectra.
  • AFNI - AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data.
  • Sparky - Sparky is the most popular NMR analysis tool for biomolecules for more than a decade.
  • NMRFAM-Sparky - Sparky is the most popular NMR analysis tool for biomolecules for more than a decade. NMRFAM has taken over the original Sparky from UCSF for the continuous development to implement advances in biomolecular NMR field. Thanks to the generous allowance of Tom Goddard and Tom Ferrin from UCSF, NMRFAM is official center for developing, maintaining and distributing the new version of Sparky that we call it NMRFAM-SPARKY.
  • POKY - A software suite for multidimensional NMR, 3D structure calculation of biomolecules and more!
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