Journal ArticleDOI
Torsion angle dynamics for nmr structure calculation with the new program dyana
TLDR
Test calculations starting from conformers with random torsion angle values showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures.About:
This article is published in Journal of Molecular Biology.The article was published on 1997-10-17. It has received 2768 citations till now. The article focuses on the topics: Dihedral angle.read more
Citations
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Journal ArticleDOI
The CCPN data model for NMR spectroscopy: Development of a software pipeline
Wim F. Vranken,Wayne Boucher,Tim J. Stevens,Rasmus H. Fogh,Anne Pajon,Miguel Llinás,Eldon L. Ulrich,John L. Markley,John Ionides,Ernest D. Laue +9 more
TL;DR: The development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach and providing a pipeline for high‐throughput analysis of NMR data.
Journal ArticleDOI
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
TL;DR: The CANDID approach has further been validated by de novo NMR structure determinations of four additional proteins and shows that once nearly complete sequence-specific resonance assignments are available, the automated CANDIDs approach results in greatly enhanced efficiency of the NOESY spectral analysis.
Book ChapterDOI
Automated NMR structure calculation with CYANA.
TL;DR: This chapter gives an introduction to automated nuclear magnetic resonance (NMR) structure calculation with the program CYANA.
Journal ArticleDOI
NMR Solution Structure of the Human Prion Protein
Ralph Zahn,Aizhuo Liu,Thorsten Lührs,Roland Riek,Christine von Schroetter,Francisco López García,Martin Billeter,Luigi Calzolai,Gerhard Wider,Kurt Wüthrich +9 more
TL;DR: The NMR structures of the recombinant human prion protein hPrP(23-230) include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered "tail," which influences the local conformational state of the polypeptide segments.
Journal ArticleDOI
Amyloid fibrils of the HET-s(218–289) prion form a β-solenoid with a triangular hydrophobic core.
Christian Wasmer,Adam Lange,Hélène Van Melckebeke,Ansgar B. Siemer,Roland Riek,Beat H. Meier +5 more
TL;DR: A structural model based on solid-state nuclear magnetic resonance restraints for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus Podospora anserina is presented.
References
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Journal ArticleDOI
Molecular dynamics with coupling to an external bath.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Book
Mathematical Methods of Classical Mechanics
TL;DR: In this paper, Newtonian mechanics: experimental facts investigation of the equations of motion, variational principles Lagrangian mechanics on manifolds oscillations rigid bodies, differential forms symplectic manifolds canonical formalism introduction to pertubation theory.