New applications of simulated annealing in X-ray crystallography and solution NMR.
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P. Adams | A. Brünger | L. Rice | A. Brunger
[1] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[2] D. Blow,et al. The detection of sub‐units within the crystallographic asymmetric unit , 1962 .
[3] Martin Karplus,et al. Vicinal Proton Coupling in Nuclear Magnetic Resonance , 1963 .
[4] L. Verlet. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .
[5] R. Diamond. A real-space refinement procedure for proteins , 1971 .
[6] J. Curro. Computer simulation of multiple chain systems—the effect of density on the average chain dimensions , 1974 .
[7] George M. Church,et al. A structure-factor least-squares refinement procedure for macromolecular structures using constrained and restrained parameters , 1977 .
[8] J. W. Humberston. Classical mechanics , 1980, Nature.
[9] Olga Kennard,et al. Systematic analysis of structural data as a research technique in organic chemistry , 1983 .
[10] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[11] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[12] W. Hendrickson. Stereochemically restrained refinement of macromolecular structures. , 1985, Methods in enzymology.
[13] M. Rossmann,et al. The Refinement of Southern Bean Mosaic Virus in Reciprocal Space , 1984 .
[14] N Go,et al. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. , 1985, Journal of molecular biology.
[15] W F van Gunsteren,et al. A protein structure from nuclear magnetic resonance data. lac repressor headpiece. , 1985, Journal of molecular biology.
[16] K. Wüthrich. NMR of proteins and nucleic acids , 1988 .
[17] M Karplus,et al. The three‐dimensional structure of α1‐purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics , 1986, The EMBO journal.
[18] M Karplus,et al. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. , 1986, Journal of molecular biology.
[19] M Karplus,et al. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[20] R. Huber,et al. Crystal structure determination, refinement and the molecular model of the alpha-amylase inhibitor Hoe-467A. , 1986, Journal of molecular biology.
[21] Emile H. L. Aarts,et al. Simulated Annealing: Theory and Applications , 1987, Mathematics and Its Applications.
[22] H. Scheraga,et al. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[23] W. Braun,et al. Distance geometry and related methods for protein structure determination from NMR data , 1987, Quarterly Reviews of Biophysics.
[24] M. Karplus,et al. Crystallographic R Factor Refinement by Molecular Dynamics , 1987, Science.
[25] M. Saunders. Stochastic exploration of molecular mechanics energy surfaces. Hunting for the global minimum , 1987 .
[26] E. Haug,et al. A Recursive Formulation for Constrained Mechanical System Dynamics: Part II. Closed Loop Systems , 1987 .
[27] E. Haug,et al. A recursive formulation constrained mechanical system dynamics. I: Open loop systems , 1987 .
[28] A. Gronenborn,et al. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. , 1988, Protein engineering.
[29] A. Brünger. Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase. , 1988, Journal of molecular biology.
[30] A. Gronenborn,et al. Refinement of the solution structure of the DNA dodecamer 5'd(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics. , 1988, Biochemistry.
[31] A. Gronenborn,et al. Determination of three‐dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms Circumventing problems associated with folding , 1988, FEBS letters.
[32] A. Brunger. Crystallographic refinement by simulated annealing , 1988 .
[33] A. Gronenborn,et al. Determination of three‐dimensional structures of proteins from interproton distance data by hybrid distance geometry‐dynamical simulated annealing calculations , 1988, FEBS letters.
[34] Edward J. Haug,et al. A Recursive Formulation for Constrained Mechanical System Dynamics: Part III. Parallel Processor Implementation , 1988 .
[35] M G Rossmann,et al. The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure. , 1988, Acta crystallographica. Section A, Foundations of crystallography.
[36] M. Karplus,et al. Crystallographic refinement by simulated annealing: application to crambin , 1989 .
[37] Wilfred F. van Gunsteren,et al. Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .
[38] W. V. Gunsteren,et al. Testing the method of crystallographic refinement using molecular dynamics , 1989 .
[39] R. Read. Structure-factor probabilities for related structures , 1990 .
[40] A T Brünger,et al. Slow-cooling protocols for crystallographic refinement by simulated annealing. , 1990, Acta crystallographica. Section A, Foundations of crystallography.
[41] William H. Press,et al. Numerical recipes , 1990 .
[42] J. Skehel,et al. Refinement of the influenza virus hemagglutinin by simulated annealing. , 1991, Journal of molecular biology.
[43] P Gros,et al. Inclusion of thermal motion in crystallographic structures by restrained molecular dynamics. , 1990, Science.
[44] M. Karplus,et al. Molecular dynamics simulations in biology , 1990, Nature.
[45] J. Prestegard,et al. Refinement of the NMR structures for acyl carrier protein with scalar coupling data , 1990, Proteins.
[46] S H Kim,et al. Atomic charges for DNA constituents derived from single-crystal X-ray diffraction data. , 1990, Journal of molecular biology.
[47] M. Nilges,et al. Sampling Properties of Simulated Annealing and Distance Geometry , 1991 .
[48] R. Huber,et al. Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .
[49] W. Hendrickson. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. , 1991, Science.
[50] J. Zou,et al. Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.
[51] John Kuriyan,et al. Exploration of disorder in protein structures by X‐ray restrained molecular dynamics , 1991, Proteins.
[52] Jeffrey C. Hoch,et al. Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy , 1991, NATO ASI Series.
[53] G. Bricogne. A multisolution method of phase determination by combined maximization of entropy and likelihood. III. Extension to powder diffraction data , 1991 .
[54] A. Brunger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .
[55] P Argos,et al. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. , 1992, Journal of molecular biology.
[56] A. Brünger. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures , 1992, Nature.
[57] A. Gronenborn,et al. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. , 1993, Science.
[58] T. L. James,et al. Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure , 1993, Journal of biomolecular NMR.
[59] G Bricogne,et al. Direct phase determination by entropy maximization and likelihood ranking: status report and perspectives. , 1993, Acta crystallographica. Section D, Biological crystallography.
[60] Abhinandan Jain,et al. A fast recursive algorithm for molecular dynamics simulation , 1993 .
[61] Axel T. Brunger,et al. Thermal Motion and Conformational Disorder in Protein Crystal Structures: Comparison of Multi‐Conformer and Time‐Averaging Models , 1994 .
[62] Abhinandan Jain,et al. Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton‐Euler inverse mass operator method for internal coordinate dynamics , 1994, Proteins.
[63] G W Vuister,et al. The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR. , 1994, Journal of magnetic resonance. Series B.
[64] D F Mierke,et al. Coupling constants again: Experimental restraints in structure refinement , 1994, J. Comput. Aided Mol. Des..
[65] A. Brünger,et al. Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement , 1994, Proteins.
[66] A M Gronenborn,et al. The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR. , 1995, Journal of magnetic resonance. Series B.
[67] Angela M. Gronenborn,et al. The Impact of Direct Refinement against 13Cα and 13Cβ Chemical Shifts on Protein Structure Determination by NMR , 1995 .
[68] Z. Dauter,et al. Proteins at atomic resolution. , 1995, Current opinion in structural biology.
[69] Structure determination from NOESY intensities using a metropolis simulated-annealing (MSA) refinement of dihedral angles. , 1995, Journal of magnetic resonance. Series B.
[70] M Nilges,et al. Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. , 1995, Journal of molecular biology.
[71] A. Brünger,et al. Conformational variability of solution nuclear magnetic resonance structures. , 1995, Journal of molecular biology.
[72] Full-matrix refinement of the protein crambin at 0.83 A and 130 K. , 1995, Acta crystallographica. Section D, Biological crystallography.
[73] Eric Oldfield,et al. Chemical shifts and three-dimensional protein structures , 1995, Journal of biomolecular NMR.
[74] A M Gronenborn,et al. The impact of direct refinement against proton chemical shifts on protein structure determination by NMR. , 1995, Journal of magnetic resonance. Series B.
[75] M Nilges,et al. Structure calculation from NMR data. , 1996, Current opinion in structural biology.
[76] G. Kleywegt,et al. Checking your imagination: applications of the free R value. , 1996, Structure.
[77] A. Gronenborn,et al. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases , 1996, Protein science : a publication of the Protein Society.
[78] A T Brünger,et al. Do NOE distances contain enough information to assess the relative populations of multi-conformer structures? , 1996, Journal of biomolecular NMR.
[79] V S Lamzin,et al. Ribonuclease from Streptomyces aureofaciens at atomic resolution. , 1996, Acta crystallographica. Section D, Biological crystallography.
[80] R. Read,et al. Improved Structure Refinement Through Maximum Likelihood , 1996 .
[81] A T Brünger,et al. Direct Observation of Protein Solvation and Discrete Disorder with Experimental Crystallographic Phases , 1996, Science.
[82] H. Berman,et al. New parameters for the refinement of nucleic acid-containing structures. , 1996, Acta crystallographica. Section D, Biological crystallography.
[83] T. Steitz,et al. Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution , 1997, Nature Structural Biology.
[84] A T Brünger,et al. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. , 1997, Journal of magnetic resonance.
[85] R. Read,et al. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. , 1997, Proceedings of the National Academy of Sciences of the United States of America.