Search Results - "Fogh, Rasmus H."

The CCPN data model for NMR spectroscopy: Development of a software pipeline by Vranken, Wim F., Boucher, Wayne, Stevens, Tim J., Fogh, Rasmus H., Pajon, Anne, Llinas, Miguel, Ulrich, Eldon L., Markley, John L., Ionides, John, Laue, Ernest D.

“…To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR…”
Get full text

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013 by Rosato, Antonio, Vranken, Wim, Fogh, Rasmus H., Ragan, Timothy J., Tejero, Roberto, Pederson, Kari, Lee, Hsiau-Wei, Prestegard, James H., Yee, Adelinda, Wu, Bin, Lemak, Alexander, Houliston, Scott, Arrowsmith, Cheryl H., Kennedy, Michael, Acton, Thomas B., Xiao, Rong, Liu, Gaohua, Montelione, Gaetano T., Vuister, Geerten W.

“…The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten…”
Get full text

The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR by CHIGNOLA, Francesca, MARI, Silvia, STEVENS, Tim J, FOGH, Rasmus H, MANNELLA, Valeria, BOUCHER, Wayne, MUSCO, Giovanna

“…We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN…”
Get full text

CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis by Skinner, Simon P., Fogh, Rasmus H., Boucher, Wayne, Ragan, Timothy J., Mureddu, Luca G., Vuister, Geerten W.

“…NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies…”
Get full text

Structure calculation, refinement and validation using CcpNmr Analysis by Skinner, Simon P., Goult, Benjamin T., Fogh, Rasmus H., Boucher, Wayne, Stevens, Tim J., Laue, Ernest D., Vuister, Geerten W.

“…CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition,…”
Get full text

A software framework for analysing solid-state MAS NMR data by Stevens, Tim J., Fogh, Rasmus H., Boucher, Wayne, Higman, Victoria A., Eisenmenger, Frank, Bardiaux, Benjamin, van Rossum, Barth-Jan, Oschkinat, Hartmut, Laue, Ernest D.

“…Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of…”
Get full text

Straightforward and complete deposition of NMR data to the PDBe by Penkett, Christopher J, van Ginkel, Glen, Velankar, Sameer, Swaminathan, Jawahar, Ulrich, Eldon L, Mading, Steve, Stevens, Tim J, Fogh, Rasmus H, Gutmanas, Aleksandras, Kleywegt, Gerard J, Henrick, Kim, Vranken, Wim F

“…We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely…”
Get full text

WeNMR: Structural Biology on the Grid by Wassenaar, Tsjerk A., van Dijk, Marc, Loureiro-Ferreira, Nuno, van der Schot, Gijs, de Vries, Sjoerd J., Schmitz, Christophe, van der Zwan, Johan, Boelens, Rolf, Giachetti, Andrea, Ferella, Lucio, Rosato, Antonio, Bertini, Ivano, Herrmann, Torsten, Jonker, Hendrik R. A., Bagaria, Anurag, Jaravine, Victor, Güntert, Peter, Schwalbe, Harald, Vranken, Wim F., Doreleijers, Jurgen F., Vriend, Gert, Vuister, Geerten W., Franke, Daniel, Kikhney, Alexey, Svergun, Dmitri I., Fogh, Rasmus H., Ionides, John, Laue, Ernest D., Spronk, Chris, Jurkša, Simonas, Verlato, Marco, Badoer, Simone, Dal Pra, Stefano, Mazzucato, Mirco, Frizziero, Eric, Bonvin, Alexandre M. J. J.

“…The WeNMR ( http://www.wenmr.eu ) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance…”
Get full text

An overview of tools for the validation of protein NMR structures by Vuister, Geerten W., Fogh, Rasmus H., Hendrickx, Pieter M. S., Doreleijers, Jurgen F., Gutmanas, Aleksandras

“…Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11 % of all structures…”
Get full text

MEMOPS: Data modelling and automatic code generation by Fogh, Rasmus H., Boucher, Wayne, Ionides, John M.C., Vranken, Wim F., Stevens, Tim J., Laue, Ernest D.

“…In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses…”
Get full text

Erratum to: CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis by Skinner, Simon P., Fogh, Rasmus H., Boucher, Wayne, Ragan, Timothy J., Mureddu, Luca G., Vuister, Geerten W.

Get full text

Analysis of the structural quality of the CASD-NMR 2013 entries by Ragan, Timothy J., Fogh, Rasmus H., Tejero, Roberto, Vranken, Wim, Montelione, Gaetano T., Rosato, Antonio, Vuister, Geerten W.

“…We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We…”
Get full text

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework by Schneider, Olaf, Fogh, Rasmus H, Sternberg, Ulrich, Klenin, Konstantin, Kondov, Ivan

“…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…”
Get more information

nomenclature and data model to describe NMR experiments by Fogh, Rasmus H, Vranken, Wim F, Boucher, Wayne, Stevens, Tim J, Laue, Ernest D

“…Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason…”
Get full text

The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer by Brasher, Sally V., Smith, Brian O., Fogh, Rasmus H., Nietlispach, Daniel, Thiru, Abarna, Nielsen, Peter R., Broadhurst, R. William, Ball, Linda J., Murzina, Natalia V., Laue, Ernest D.

Get full text

A framework for scientific data modeling and automated software development by Fogh, Rasmus H., Boucher, Wayne, Vranken, Wim F., Pajon, Anne, Stevens, Tim J., Bhat, T. N., Westbrook, John, Ionides, John M. C., Laue, Ernest D.

“…Motivation: The lack of standards for storage and exchange of data is a serious hindrance for the large-scale data deposition, data mining and program…”
Get full text

MEMOPS: Data modelling and automatic code generation by Fogh, Rasmus H., Boucher, Wayne, Ionides, John M.C., Vranken, Wim F., Stevens, Tim J., Laue, Ernest D.

“…In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses…”
Get full text

NMR Exchange Format: a unified and open standard for representation of NMR restraint data by Gutmanas, Aleksandras, Adams, Paul D, Bardiaux, Benjamin, Berman, Helen M, Case, David A, Fogh, Rasmus H, Güntert, Peter, Hendrickx, Pieter M S, Herrmann, Torsten, Kleywegt, Gerard J, Kobayashi, Naohiro, Lange, Oliver F, Markley, John L, Montelione, Gaetano T, Nilges, Michael, Ragan, Timothy J, Schwieters, Charles D, Tejero, Roberto, Ulrich, Eldon L, Velankar, Sameer, Vranken, Wim F, Wedell, Jonathan R, Westbrook, John, Wishart, David S, Vuister, Geerten W

“…We present here a unified, easily adaptable, open-source NMR exchange format (NEF) for NMR restraints and associated data…”
Get full text

The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer by Brasher, Sally V., Smith, Brian O., Fogh, Rasmus H., Nietlispach, Daniel, Thiru, Abarna, Nielsen, Peter R., Broadhurst, R. William, Ball, Linda J., Murzina, Natalia V., Laue, Ernest D.

“…The heterochromatin protein 1 (HP1) family of proteins is involved in gene silencing via the formation of heterochromatic structures. They are composed of two…”
Get full text

Sequence-specific proton NMR assignments and secondary structure in the sea anemone polypeptide Stichodactyla helianthus neurotoxin I by Fogh, Rasmus H, Mabbutt, Bridget C, Kem, William R, Norton, Raymond S

Get full text