Relevant bibliographies by topics / NMR structure refinement

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'NMR structure refinement'

Author: Grafiati
Published: 10 March 2023

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Journal articles on the topic "NMR structure refinement"

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Skinner, Simon P., Benjamin T. Goult, Rasmus H. Fogh, Wayne Boucher, Tim J. Stevens, Ernest D. Laue, and Geerten W. Vuister. "Structure calculation, refinement and validation usingCcpNmr Analysis." Acta Crystallographica Section D Biological Crystallography 71, no. 1 (January 1, 2015): 154–61. http://dx.doi.org/10.1107/s1399004714026662.

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CcpNmr Analysisprovides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes howCcpNmr Analysiscan seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral, hydrogen bonds and residual dipolar couplings (RDCs)], exporting these to and subsequently re-importing them from structure-calculation software (such as the programsCYANAorARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements toCcpNmr Analysisdescribed here, this process is now much more intuitive and efficient and less error-prone.
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Scarperi, Andrea, Giovanni Barcaro, Aleksandra Pajzderska, Francesca Martini, Elisa Carignani, and Marco Geppi. "Structural Refinement of Carbimazole by NMR Crystallography." Molecules 26, no. 15 (July 29, 2021): 4577. http://dx.doi.org/10.3390/molecules26154577.

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The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave’s disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.
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Ikeya, Teppei, Shiro Ikeda, Takanori Kigawa, Yutaka Ito, and Peter Güntert. "Protein NMR Structure Refinement based on Bayesian Inference." Journal of Physics: Conference Series 699 (March 2016): 012005. http://dx.doi.org/10.1088/1742-6596/699/1/012005.

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Laws, David D., Angel C. de Dios, and Eric Oldfield. "NMR chemical shifts and structure refinement in proteins." Journal of Biomolecular NMR 3, no. 5 (September 1993): 607–12. http://dx.doi.org/10.1007/bf00174614.

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CUI, FENG, ROBERT JERNIGAN, and ZHIJUN WU. "KNOWLEDGE-BASED VERSUS EXPERIMENTALLY ACQUIRED DISTANCE AND ANGLE CONSTRAINTS FOR NMR STRUCTURE REFINEMENT." Journal of Bioinformatics and Computational Biology 06, no. 02 (April 2008): 283–300. http://dx.doi.org/10.1142/s0219720008003448.

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Nuclear Overhauser effects (NOE) distance constraints and torsion angle constraints are major conformational constraints for nuclear magnetic resonance (NMR) structure refinement. In particular, the number of NOE constraints has been considered as an important determinant for the quality of NMR structures. Of course, the availability of torsion angle constraints is also critical for the formation of correct local conformations. In our recent work, we have shown how a set of knowledge-based short-range distance constraints can also be utilized for NMR structure refinement, as a complementary set of conformational constraints to the NOE and torsion angle constraints. In this paper, we show the results from a series of structure refinement experiments by using different types of conformational constraints — NOE, torsion angle, or knowledge-based constraints — or their combinations, and make a quantitative assessment on how the experimentally acquired constraints contribute to the quality of structural models and whether or not they can be combined with or substituted by the knowledge-based constraints. We have carried out the experiments on a small set of NMR structures. Our preliminary calculations have revealed that the torsion angle constraints contribute substantially to the quality of the structures, but require to be combined with the NOE constraints to be fully effective. The knowledge-based constraints can be functionally as crucial as the torsion angle constraints, although they are statistical constraints after all and are not meant to be able to replace the latter.
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Sinelnikova, Anna, and David van der Spoel. "NMR refinement and peptide folding using the GROMACS software." Journal of Biomolecular NMR 75, no. 4-5 (March 28, 2021): 143–49. http://dx.doi.org/10.1007/s10858-021-00363-z.

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AbstractNuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins and nucleic acids. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.
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Clore, G. M., and A. M. Gronenborn. "New methods of structure refinement for macromolecular structure determination by NMR." Proceedings of the National Academy of Sciences 95, no. 11 (May 26, 1998): 5891–98. http://dx.doi.org/10.1073/pnas.95.11.5891.

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Schwieters, Charles D., and G. Marius Clore. "The VMD-XPLOR Visualization Package for NMR Structure Refinement." Journal of Magnetic Resonance 149, no. 2 (April 2001): 239–44. http://dx.doi.org/10.1006/jmre.2001.2300.

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Bestaoui, Naima, Xiang Ouyang, Florence Fredoueil, Bruno Bujoli, and Abraham Clearfield. "Structural characterization of Cd3(O3PC2H4CO2)2·2H2O from in-house X-ray powder data and NMR." Acta Crystallographica Section B Structural Science 61, no. 6 (November 14, 2005): 669–74. http://dx.doi.org/10.1107/s0108768105028387.

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The title compound poly[[bis(μ-2-carboxylatoethylphosphonato)cadmium] dihydrate], Cd3(O3PC2H4CO2)2·2H2O, was prepared by a hydrothermal reaction and its crystal structure determined from in-house powder data. The structure was solved in both P21/c and P21 space groups. The refinement converged with Rp = 0.1046, R wp = 0.1378 and Rf = 0.0763 in P21/c. However, the solid-state NMR data could not be explained. The structure was then solved in P21 and the refinement converged with Rp = 0.0750, R wp = 0.1022 and Rf = 0.0409 and satisfied the NMR requirements.
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Neuberger, Sven, Sean P. Culver, Hellmut Eckert, Wolfgang G. Zeier, and Jörn Schmedt auf der Günne. "Refinement of the crystal structure of Li4P2S6 using NMR crystallography." Dalton Transactions 47, no. 33 (2018): 11691–95. http://dx.doi.org/10.1039/c8dt02619j.

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Dissertations / Theses on the topic "NMR structure refinement"

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Ball, Graeme. "Structure refinement and dynamics of proteins using residual dipolar couplings and NMR relaxation data." Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/10718.

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NMR spectroscopy can be used to investigate the structure and dynamics of proteins, both of which can provide important insights into their functions. The aims of this project were to use residual dipolar coupling (RDC) restraints to refine the existing NMR structures of several proteins and to use relaxation data to investigate their dynamics. Three proteins were studied: two module-pair fragments from human complement regulatory proteins (DAF ~ 2,3 and C4BP~1,2) and a fatty acid binding protein from the nematode parasite Ascaris suum (ABA-1A), each of which consists of two structural elements, with a poorly defined relative orientation. Implementing experiments required for the measurement of coupling constraints led to the development of new methods for the determination of the one-bond 1DCαHαRDC. Extensive sets of RDCs were measured for C4BP~1,2 and ABA-1A using 15N and 13C labelled samples and the structure refinement protocol incorporating RDCs as restraints was optimised. Significant improvements in the quality of the refined structures were achieved. The backbone dynamics of DAF~2,3 and C4BP~1,2 were probed using relaxation data measured at two fields and the time scale and extent of back-bone motions were quantified. Finally, some evidence of small amplitude intermodular motions in the module-pair proteins DAF~2,3 and C4BP~1,2 was observed. The functional significance of these findings is discussed.
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Cui, Feng. "Distance-based NMR structure determination and refinement /." 2005.

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RINALDELLI, MAURO. "Development of software tools for protein structural and dynamic characterization." Doctoral thesis, 2014. http://hdl.handle.net/2158/835698.

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In this thesis I focused on the development of novel bioinformatic tools for the structural characterization of proteins. The protein structure of MMP-12 in solid state has been calculated and its crystal packing has been reconstructed using distance restraints and pseudocontact shifts (pcs), by implementing in Cyana a protocol for the simultaneous analysis of the intermolecular and intramolecular contributions to the pcs. The use of pcs and residual dipolar couplings (rdc) has been implemented in the program REFMAC5, for a joint refinement against X-ray and NMR data. A web portal for the analysis of paramagnetic data against the molecular structures has been developed.
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Wylie, Benjamin. "Solid-state magic-angle spinning NMR methods for tensor measurements and protein structure refinement using chemical shift tensors /." 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3314941.

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Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2008.
Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 3023. Adviser: Chad M. Rienstra. Includes bibliographical references (leaves 222-233). Available on microfilm from Pro Quest Information and Learning.
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Book chapters on the topic "NMR structure refinement"

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Vranken, Wim F., Geerten W. Vuister, and Alexandre M. J. J. Bonvin. "NMR-Based Modeling and Refinement of Protein 3D Structures." In Methods in Molecular Biology, 351–80. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1465-4_16.

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Torda, Andrew E., Ruud M. Scheek, and Wilfred F. van Gunsteren. "Time Averaged Distance Restraints in NMR Based Structural Refinement." In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, 219–25. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4757-9794-7_16.

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James, Thomas L., Miriam Gochin, Deborah J. Kerwood, David A. Pearlman, Uli Schmitz, and Paul D. Thomas. "Refinement of Three-Dimensional Protein and DNA Structures in Solution from NMR Data." In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, 331–47. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4757-9794-7_25.

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Habazettl, J., M. Nilges, H. Oschkinat, A. T. Brünger, and T. A. Holak. "NMR Structures of Proteins Using Stereospecific Assignments and Relaxation Matrix Refinement in a Hybrid Method of Distance Geometry and Simulated Annealing." In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy, 395–408. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4757-9794-7_31.

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Braun, Werner, Otto Epp, Kurt Wüthrich, and Robert Huber. "Solution of the Phase Problem in the X-ray Diffraction Method for Proteins with the Nuclear Magnetic Resonance Solution Structure as Initial Model: Patterson Search and Refinement for the α-Amylase Inhibitor Tendamistat." In NMR in Structural Biology, 356–63. WORLD SCIENTIFIC, 1995. http://dx.doi.org/10.1142/9789812795830_0028.

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Pérez Méndez, Mercedes, José Fayos Alcañiz, and Marc Meunier. "Molecular Simulation of Cholesteric Liquid-Crystal Polyesteramides: Conformational and Structure Analysis by Rietveld Refinement." In Liquid Crystals [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.100388.

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Molecular modeling techniques are applied to polyesteramides designed as PNOBDME (C34H38N2O6)n and PNOBEE (C26H22N2O6)n, synthesized and characterized as cholesteric liquid crystals -through the condensation reaction between 4 and 4′-(terephthaloyl- diaminedibenzoic chloride (NOBC) and racemic glycol: DL-1,2 dodecanediol, or DL-1,2-butanediol, respectively, being chemical modifications of precursor multifunctional cholesteric LC polyesters, adding new properties but holding their helical macromolecular structures. Although the starting raw materials were racemic, these cholesteric LC polymers exhibit unexpected optical activity and chiral morphology. For that reason, conformational analysis is studied on the monomer models of PNOBDME and PNOBEE. Four helical conformers models, experimentally observed by NMR, are proposed for each cholesteric polyesteramide: Rgg, Rgt, Sgg, Sgt. Polymerization of the monomeric conformers, with minima energies, have been simulated and used to reproduce the crystalline fraction observed by x-ray diffraction. Three orders of chirality are observed in the structure of the polymer chains: One due to the asymmetric carbon atoms, a second chirality due to the two successive rotations of the benzene groups, along the main chain, within the monomer which implies the formation of helical molecules, for both R and S chirality and still, a third chirality corresponding to the twisting of the rigid/semirigid cholesteric LC polymer chains. All these factors contributing to the net optical activity observed in these materials. Crystal packing is simulated in triclinic primitive P1cells, with molecular chains oriented parallel to the z-axis (c lattice parameter equal to the pitch length of each simulated polymer helix) and parameters a, b, α, β and γ, obtained by Pawley refinement from the known structures of precursor polyesters. The simulated x-ray diffraction patterns of the proposed crystal models fit, after successive Pawley and Rietveld refinement cycles, the experimental WAXS. Powder Quantitative Phase Analysis applied to an ideal mixture with the four possible helical conformers, for each degree of polymerization, allows to refine their relative weight and determine the major phase relative amount. These results would confirm the theory of a preferable recrystallization, among the four possible helical diastereoisomers, depending on the synthetic conditions.
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Conference papers on the topic "NMR structure refinement"

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Milner, Justin L., and Fadi Abu-Farha. "On the Manufacture of Lightweight Alloy Tubes via Friction Stir Back Extrusion: Process Evaluation and Material Performance." In ASME 2014 International Manufacturing Science and Engineering Conference collocated with the JSME 2014 International Conference on Materials and Processing and the 42nd North American Manufacturing Research Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/msec2014-4148.

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A new manufacturing approach in which the friction stirring phenomenon is used as a vehicle for facilitating the deformation of bulk lightweight materials into manufactured components has been recently introduced under the general concept of “bulk friction stir forming”. In a preliminary work, the concept was applied to the back extrusion process, in what was referred to as “friction stir back extrusion” or FSBE; it was shown that the concept is practically valid and FSBE is capable of producing lightweight tubular specimens. Nevertheless, the FSBE process was claimed to have several merits over conventional processes, mainly: (i) unique process capabilities and energy efficiency (ii) significant grain refinement, and thus (iii) favorable mechanical properties in the formed tubes. None of these claims were adequately addressed nor quantified in earlier work. Therefore, this work presents a comprehensive study that aims to reveal the true merits of FSBE, validate the claims, and quantify its effects on the microstructure and mechanical properties of the deformed material. The outcomes of the study are presented in three major parts, each addressing one of the abovementioned claims. Force, torque and power measurements during FSBE experiments are used to address the first claim. Detailed optical microscopy and electron back scatter diffraction work is carried out in the second part to quantify the changes to the grain structure and texture of the material. Finally, the third part presents detailed mechanical characterization using digital image correlation to quantify the effects of FSBE on the performance of the produced tubes.
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Limchuchua, Kittipong, Sawatdiwong Sarisittitham, Pichaya Ruthairung, Jugkapun Whangkitjamorn, Nuddanet Sikharin, Nitshakhan Jitpipatpong, and Pannayod Kritsadativud. "Tight Reservoir Automatic 3D-Modelling Generator: Turning Complicated into Effortless Application." In International Petroleum Technology Conference. IPTC, 2023. http://dx.doi.org/10.2523/iptc-22965-ea.

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Abstract Because tight reservoir has become important energy resources in sustaining production, PTTEP has recently evaluated a number of these reservoirs. For development plan optimization and resources estimation, 3D-modelling is the most efficient tool. However, the complicated workflow usually impedes inexperienced users to work with reservoir simulation. This study aims to construct an automatic 3D-modelling generator which could handle the tight reservoir. This would allow non-simulation expert to construct any 3D models for further simulation study. In this study, black oil simulation model is selected for simplicity. A generic multi-layer tight reservoir model is consisted of cartesian grids with the local grid refinement (LGR) at a well location to capture flow regime near a hydraulic fracture. The user interface tabs contain input spreadsheet for grid design, rock and fluid properties, initial conditions, well completion, and production schedule. Then, the script files with black oil simulator keywords will be generated. The capability to adjust all the input data is finally introduced to ensure user-friendly interface before finalizing the script files to simulation software without any complication with the simulation keywords. With the created Tight Reservoir Automatic 3D-Modelling Generator, all complicated workflows (the black oil simulator keywords and structure) are handled. The 3D modelling for tight reservoir does not require highly experienced user anymore. Also, neither high expertise in simulation nor programming is required. The generator provides user friendly interface with full capability of automatic multi-layer model construction. It also can handle any kind of fluid system (oil/gas/water and saturated/undersaturated reservoir), and the presence of a hydraulic fracture in any specific layers. In terms of the well and production control, it provides the option frequently used e.g., control BHP, control THP, control flow rate. This generator has been used in several PTTEP projects which have proven the success of the application. Currently, for the high-level field evaluation of the tight reservoir, any inexperienced user could construct the 3D model for their usage without having to request support from the simulation team. Regarding this advantage, there has been measurable manpower saving for model construction. Therefore, user could have more time to focus on engineering analysis such as sensitivity study on relevant parameters or production forecast and optimization which ultimately bring the best value for the project evaluation. Although commercial software may be available, they require costs and learning. Also, that software may not fully fit with specific objective. With in-house development of this pre-processer modeling tool, the interface is proven to be ease of use and fit-for-purpose with no additional cost. Further improvement would easily be performed. The concept of coupling the familiar user interface with reservoir simulator could be extended to other opportunity not only in PTTEP, but also anywhere else.
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