Journal ArticleDOI
Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm.
Werner Braun,Nobuhiro Go +1 more
TLDR
A method to determine the three-dimensional structure of a protein molecule from such a set of distance constraints as can be determined by nuclear magnetic resonance studies, applicable to large molecules, with all atoms treated explicitly.About:
This article is published in Journal of Molecular Biology.The article was published on 1985-12-05. It has received 550 citations till now. The article focuses on the topics: Metric (mathematics).read more
Citations
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Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Journal ArticleDOI
Comparative protein structure modeling using Modeller.
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Journal ArticleDOI
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
David A. Pearlman,David A. Case,James W. Caldwell,Wilson S. Ross,Thomas E. Cheatham,Steve DeBolt,David M. Ferguson,George Seibel,Peter A. Kollman +8 more
TL;DR: The development, current features, and some directions for future development of the AMBER package of computer programs are described, embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.
Journal ArticleDOI
Torsion angle dynamics for nmr structure calculation with the new program dyana
TL;DR: 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.
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The GROMOS Biomolecular Simulation Program Package
Walter R. P. Scott,Philippe H. Hünenberger,Ilario G. Tironi,Alan E. Mark,S. R. Billeter,Jens Fennen,Andrew E. Torda,Thomas Huber,Peter Kruger,W. F. van Gunsteren +9 more
TL;DR: The newest version of the GROningen MOlecular Simulation program package, GROMOS96, has been developed for the dynamic modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism.
References
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Journal ArticleDOI
Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
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Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
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Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.
TL;DR: "Pseudo-structures" of the 20 common amino acid residues are introduced for use in protein spatial structure determinations, which rely on the use of intramolecular proton-proton distance constraints determined by nuclear Overhauser effects as input for distance geometry calculations.
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Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids
Journal ArticleDOI
Crystallographic refinement of the structure of bovine pancreatic trypsin inhibitor at l.5 Å resolution
Johann Deisenhofer,W. Steigemann +1 more
TL;DR: In this article, the model of pancreatic trypsin inhibitor determined by Huber, Kukla, Rtihlmann, Epp & Formanek [Naturwissenschaften (1970). 57, 389-392] was fitted to an electron density map of 1.9 A resolution calculated with isomorphous-replacement phases by application of the real-space refinement procedure of Diamond [Acta Cryst. (1971). A27, 436-452].