Topic
Collaborative Computing Project for NMR
About: Collaborative Computing Project for NMR is a research topic. Over the lifetime, 4 publications have been published within this topic receiving 583 citations.
Papers
TL;DR: This work presents version 2.1 of ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation and reports on recent developments, most notably a graphical user interface.
Abstract: Summary: Modern structural genomics projects demand for integrated methods for the interpretation and storage of nuclear magnetic resonance (NMR) data Here we present version 21 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for automated assignment of nuclear Overhauser enhancement (NOE) data and NMR structure calculation We report on recent developments, most notably a graphical user interface, and the incorporation of the object-oriented data model of the Collaborative Computing Project for NMR (CCPN) The CCPN data model defines a storage model for NMR data, which greatly facilitates the transfer of data between different NMR software packages
Availability: A distribution with the source code of ARIA 21 is freely available at http://wwwpasteurfr/recherche/unites/Binfs/aria2
Contact: [email protected]
554 citations
Journal Article•
TL;DR: An overview of the methodology and a roadmap for future developments and applications of COSMOS-NMR, which allows introducing NMR parameters as constraints into molecular mechanics calculations, is given.
Abstract: The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.
5 citations
TL;DR: This resource is presented here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR)
Abstract: Summary: We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR) (Vranken et al., 2005, The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687–696). The project consists of a database of assigned 1D and 2D spectra of many common metabolites. The project aims to help the user to analyze and assign 1D and 2D NMR spectra of unknown metabolite mixtures. Spectra of unknown mixtures can be easily superimposed and compared with the database spectra, thus facilitating their assignment and identification.
Availability: The CCPN Metabolomics Project, together with an annotated example dataset, is freely available via: http://www.ccpn.ac.uk/metabolomics/.
Contact:mari.silvia@hsr.it (experiments & protocol); tjs23@cam.ac.uk (software).
Supplementary Information:Supplementary data are available at Bioinformatics online.
TL;DR: A recent workshop discusses the progress toward integrating NMR data into a unifying data model and the need for further research into this area.
Abstract: A recent workshop discusses the progress toward integrating NMR data into a unifying data model.
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2012 | 1 |
| 2011 | 1 |
| 2007 | 1 |
| 2002 | 1 |