Crystallographic R Factor Refinement by Molecular Dynamics

Keywords

Molecular dynamics, RADIUS, Angstrom, Macromolecule, Convergence (economics)

References

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• Stereochemically restrained refinement of macromolecular structures.Wayne A. Hendrickson — 1985
• Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin.Axel T. Brünger, G. Marius Clore, Angela M. Gronenborn — 1986
• Optimization by Simulated AnnealingScott Kirkpatrick, C. D. Gelatt, M.P. Vecchi — 1983
• A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parametersJoel L. Sussman, Stephen R. Holbrook, George M. Church — 1977
• On the polarization factor for crystal‐monochromated X‐radiation. II. A method for determining the polarization ratio for crystal monochromatorsM. G. Vincent, H. D. Flack — 1980
• Crystal structure determination, refinement and the molecular model of the alpha-amylase inhibitor Hoe-467A.J. W. Pflugrath, Georg Wiegand, Robert Huber — 1986
• Refinement of Large Structures by Simultaneous Minimization of Energy and R FactorA. Jack, Michael Levitt — 1978
• Dynamics of proteins: elements and function.M. Kurplus, J. Andrew McCammon — 1983
• CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsBernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson — 1983
• Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones MoleculesLoup Verlet — 1967

Cited by

• Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics.José María Díaz Bardales — 1992
• Crystal structures at 2.2 A resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP.Juan Fernando Ortega Muñoz — 1991
• Molecular modeling studies of novel retro-binding tripeptide active-site inhibitors of thrombin.Lúcia Amante — 1995
• A common protein fold and similar active site in two distinct families of β-glycanasesVito Carrescia, G. Corbellini, Pablo Giuliano — 1996
• Salt bridge relay triggers defective LDL receptor binding by a mutant apolipoprotein.暁子 尾本, 博志 加来, 信栄 鶴岡 — 1994
• Biological implications of a 3 A structure of dimeric antithrombin.Jérémy Boissevain — 1994
• Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase IPascal Courty — 1994
• Crystal structure of selenosubtilisin at 2.0-A resolution.Alicia González Pérez — 1993
• Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.William A. Gamson — 1996
• Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450.W. S. C. Copeman — 1996
• The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile.Sergio García Díez — 1997
• The activation domain of the MotA transcription factor from bacteriophage T4Audria Albuquerque Leal — 1997
• X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase.剛 山岸 — 1997
• Crystal structure and mechanism of human L‐arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesisÉric Spalding — 1998
• RNA-RNA interactions between oligonucleotide substrates for aminoacylation.Barry Henderson, Paul Schimmel — 1997
• Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl‐tRNA hydrolaseA. Anonymus — 1997
• The structures of thymidine kinase from Herpes simplex virus type 1 in complex with substrates and a substrate analogueJ. Sánchez Morcillo, E. Jiménez Caballero — 1997
• Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.文子 清水, 一博 中嶋, 孝 小松 — 1997
• The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 A resolution: multiple copy flexibility and receptor binding.Lars Trägårdh — 1997
• The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide.友之 中尾, 卓 坂牛 — 1998

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