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Bibliography

Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, N.F., DiNola, A., and Haak, J.R. (1984). ``Molecular dynamics with coupling to an external bath", J. Chem. Phys. 81, 3684--3690.

Bernstein, R., Ross, A., Cieslar, C., and Holak, T. A. (1992). ``A Practical Approach to Calculations of Biomolecular Structures from Homonuclear Three-Dimensional NOE-NOE Spectra", J. Magn. Reson., in press.

Bricogne, G. (1976). ``Methods and Programs for Direct-Space Exploitation of Geometric Redundancies", Acta Cryst. A32, 832--847.

Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., and Karplus, M. (1983). ``CHARMM: A Program for Macromolecular Energy, Minimization, and Molecular Dynamics Calculations", J. Comp. Chem. 4, 187--217.

Brünger, A.T. (1988). ``Crystallographic Refinement by Simulated Annealing: Application to a 2.8 Å Resolution Structure of Aspartate Aminotransferase", J. Mol. Biol. 203, 803--816.

Brünger, A.T. (1989). ``A Memory-Efficient Fast Fourier Transformation Algorithm for Crystallographic Refinement on Supercomputers", Acta Cryst. A45, 42--50.

Brünger, A.T. (1990). ``Extension of Molecular Replacement: A New Search Strategy based on Patterson Correlation Refinement", Acta Cryst. A46, 46--57.

Brünger, A.T. (1991a). ``Crystallographic Phasing and Refinement of Macromolecules", Current Opinion in Structural Biology 1, 1016--1022.

Brünger, A.T. (1991b). ``Simulated Annealing in Crystallography", Ann. Rev. Phys. Chem. 42, 197--223.

Brünger, A.T. (1991c). ``Solution of a Fab (26-10) /Digoxin Complex by Generalized Molecular Replacement", Acta Cryst. A47, 195--204.

Brünger, A.T. (1992). ``The Free R value: a Novel Statistical Quantity for Assessing the Accuracy of Crystal Structures", Nature 355, 472--474.

Brünger, A.T. (1993). ``Assessment of Phase Accuracy by Cross Validation: The Free R Value. Methods and Applications", Acta Cryst. D, in press.

Brünger, A.T., Brooks, C.L., and Karplus, M. (1984). ``Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of ST2 Water", Chem. Phys. Lett. 105, 495--500.

Brünger, A.T., Clore, G.M., Gronenborn, A.M., and Karplus, M. (1986). ``Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin", Proc. Natl. Acad. Sci. USA 83, 3801--3805.

Brünger, A.T., Clore, G.M., Gronenborn, A.M., and Karplus, M. (1987). ``Solution conformations of a human growth hormone releasing factor: comparison of the restrained molecular dynamics and distance geometry methods for a system without long-range distance data", Protein Engineering 1, 399--406.

Brünger, A.T. and Karplus, M. (1991). ``Molecular Dynamics Simulations with Experimental Restraints", Accounts Chemical Research 24 , 54--61.

Brünger, A.T. and Karplus, M. (1988). ``Polar hydrogen positions in proteins: Empirical energy function placement and neutron diffraction comparison", Proteins 4,148--156.

Brünger, A.T., Karplus, M., and Petsko, G.A. (1989). ``Crystallographic Refinement by Simulated Annealing: Application to a 1.5 Å\ Resolution Structure of Crambin", Acta Cryst. A45, 50--61.

Brünger, A. T., Krukowski, A., and Erickson, J. (1990). ``Slow-Cooling Protocols for Crystallographic Refinement by Simulated Annealing", Acta Cryst. A46, 585--593.

Brünger, A.T., Kuriyan, J., and Karplus, M. (1987). ``Crystallographic R Factor Refinement by Molecular Dynamics", Science 235, 458--460.

Brünger, A.T., Leahy, D.J., Hynes, T.R., and Fox, R.O. (1991). ``The 2.9 Å Resolution Structure of an Anti-Dinitrophenyl-Spin-Label Monoclonal Antibody Fab Fragment with Bound Hapten", J. Mol. Biol. 221 , 239--256.

Brukert, U. and Allinger, N.L. (1982). In: Molecular Mechanics, ACS Monograph 177, American Chemical Society, Washington.

Clore, G.M., Appella, E., Yamada, M., Matsushima, K., and Gronenborn, A.M. (1990). ``Three-Dimensional Structure of Interleukin 8 in Solution", Biochemistry 29, 1689--1696.

Clore, G.M. and Gronenborn, A.M. (1989). ``Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy", CRC Critical Reviews in Biochemistry 24, 479--564.

Clore, G.M. and Gronenborn, A.M. (1991). ``Structures of Larger Proteins in Solution: Three- and Four-Dimensional Heteronuclear NMR Spectroscopy", Science 252, 1390--1399.

Cremer, D. and Pople, J.A. (1975). ``General Definition of Ring Puckering Coordinates", J. Am. Chem. Soc. 97, 1354--1358.

Crippen, G. and Havel T. (1988). Distance Geometry and Molecular Conformation. Research Studies Press: Taunton, Somerset, England.

Engh, R.A. and Huber, R. (1991). ``Accurate Bond and Angle Parameters for X-ray Protein-Structure Refinement", Acta Cryst. A47, 392--400.

Ernst, R.R., Bodenhausen, G., and Wokaun, A. (1987). Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Oxford: Clarendon Press.

Goldstein, H. (1980). Classical Mechanics. New York: Addison-Wesley, chap. 4.

Gronenborn, A.M., Filpula, D.R., Essig, N.Z., Achari, A., Whitlow, M., Wingfield, P.T., and Clore, G.M. (1991). ``The immunoglobulin binding domain of streptococcal protein G has a novel and highly stable polypeptide fold", Science 253, 657--661.

Ha, S.N., Giammona, A., Field, M. and Brady, J.W. (1988). ``A Revised Potential Energy Surface for Molecular Mechanics Studies of Carbohydrates", Carbohydrate Res. 180, 207--221.

Habazettl, J., Cieslar, C., Oschkinat, H., and Holak, T.A. (1990). ``H-1-NMR Assignments of Side-Chain Conformations in Proteins Using a High-Dimensional Potential in the Simulated Annealing Calculations", FEBS Lett. 268, 141--145.

Habazettl, J., Ross, A., Oschkinat, H. and Holak, T. A. (1992a). ``Secondary NOE pathways in 2D NOESY spectra of proteins estimated from homonuclear three-dimensional NOE-NOE nuclear magnetic resonance spectroscopy", J. Magn. Reson. 97, 281--294.

Habazettl, J., Schleicher, M., Otlewski, J., and Holak, T. A. (1992b). ``Homonuclear Three-Dimensional NOE-NOE NMR Spectra for Structure Determination of Proteins in Solution", J. Mol. Biol., in press.

Hahn, T., ed. (1987). International Tables for Crystallography, Vol. A. , D. Reidel Publishing Company.

Havel, T.F. and Wüthrich, K. (1984). ``A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular HH proximities in solution" Bull. Math. Bio. 46, 673--698.

Head-Gordon, T. and Brooks, C.L. (1991). ``Virtual Rigid Body Dynamics", Biopolymers 31, 77--100.

Hendrickson, W.A. (1985). ``Stereochemically Restrained Refinement of Macromolecular Structures", Meth. Enzymol. 115, 252--270.

Hendrickson, W.A. and Ward, K.B. (1976). ``A Packing Function for Delimiting the Allowable Locations of Crystallized Macromolecules", Acta Cryst. A32, 778--780.

Hirshfeld, F.L. (1968). ``Symmetry in the Generation of Trial Structures", Acta Cryst. A 24, 301--311.

Hodel, A., Kim, S.-H., and Brünger, A.T. (1992). ``Model Bias in Macromolecular Crystal Structures", Acta Cryst. A, in press.

Huber, R. (1985). ``Experience with the application of Patterson search techniques", Molecular Replacement, (Machin, P.A., comp.), Proceedings of the Daresbury Study Weekend, Science and Engineering Research Council, The Librarian, Daresbury Laboratory, Daresbury, United Kingdom, 58--61.

James, T.L., Gochin, M., Kerwood, D.J., Schmitz, U., and Thomas, P.D. (1991). In: Computational Aspects of the Study of Biological Macromolecules by NMR, (J.C. Hoch, ed.). New York: Plenum Press.

Jorgensen, W., Chandrasekar, J., Madura, J., Impey, R., and Klein, M. (1983). ``Comparison of simple potential functions for simulating liquid water", J. Chem. Phys. 79, 926--935.

Jorgensen, W. and Tirado-Rives, J. (1988). ``The OPLS potential function for proteins, energy minimization for crystals of cyclic peptides and crambin", J. Am. Chem. Soc. 110, 1657--1666.

Kabsch, W. (1976). ``A Solution for the Best Rotation to Relate Two Sets of Vectors.", Acta Cryst. A32, 922.

Kaptein, R., Zuiderweg, E.R.P., Scheek, R.M., Boelens, R., and van Gunsteren, W.F. (1985). ``A protein structure from NMR data. lac Repressor headpiece", J. Mol. Biol. 182, 179--182.

Karplus, M. and Petsko, G.A. (1990). ``Molecular-Dynamics Simulations in Biology", Nature 347, 631--39.

Keepers, J. W. and James, T. L. (1984). ``A Theoretical Study of Distance Determinations from NMR. Two-Dimensional Nuclear Overhauser Effect Spectra", J. Magn. Reson. 57, 404--426.

Kirkpatrick, S., Gelatt, C.D.Jr., Vecchi, M.P. (1983). ``Optimization by Simulated Annealing", Science 220, 671--680.

Kuszewski, J., Nilges, M., and Brünger A.T. (1992). ``Sampling and efficiency of metric matrix distance geometry: A novel ``partial" metrization algorithm", J. Biomol. NMR 2, 33-56.

Lattman, E.E. (1985). ``Use of the Rotation and Translation Functions", Methods Enzymol. 115, 55--77.

Lee, B. and Richards, F.M. (1971). ``The Interpretation of Protein Structures: Estimation of Static Accessibility", J. Mol. Biol. 55, 379--400.

Lifson, S. and Stern, P.S. (1982). ``Born-Oppenheimer Energy Surfaces of Similar Molecules -- Interrelations Between Bond Lengths, Bond Angles, and Frequencies of Normal Vibrations in Alkanes", J. Chem. Phys. 77, 4542--4550.

Lipari, G. and Szabo, A. (1982). ``Model-Free Approach to the Interpretation of Nuclear Magnetic-Resonance Relaxation in Macromolecules .1. Theory and Range of Validity", J. Am. Chem. Soc. 104, 4546--4559.

Luzzati, P.V. (1952). ``Traitement Statistique des Erreurs dans la Determination des Structures Cristallines", Acta Cryst 5, 802--810.

Macura, S. and Ernst, R. R. (1980). ``Elucidation of Cross Relaxation in Liquids by Two-Dimensional N.M.R. Spectroscopy", Mol. Phys. 41, 95--117.

Main P. (1975). ``Recent Developments in the MULTAN System -- The Use of Molecular Structure", In "Crystallographic Computing Techniques", (Ahmed, F.R., Huml, K., Sedlácek, B., eds.), 98-103.

Morris, L., MacArthur, M.W., Hutchinson, E.G., and Thornton, J.M. (1992). Stereochemical Quality of Protein Structure Coordinates, Proteins 12, 345--364.

Naur, P. (1960). ``Revised Report on Algorithmic Language Algol-60", Computer J., 5, 349.

Némethy, G., Pottie, M.S. and Scheraga, H.A. (1983) ``Energy Parameters in Polypeptides. 9. Updating of Geometrical Parameters, Nonbonded Interactions, and Hydrogen Bond Interactions for the Naturally Occurring Amino Acids", J. Phys. Chem. 87, 1883--1887.

Nilges, M. and Brünger, A.T. (1991), J. Cellular Biochem., Supplement 15G, Abstract, CG 422, 98.

Nilges, M., Clore, G.M., and Gronenborn, A.M. (1988a). ``Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms", FEBS Lett. 239, 129--136.

Nilges, M., Clore, G.M., and Gronenborn, A.M. (1988b). ``Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations", FEBS Lett. 229, 317--324.

Nilges, M., Gronenborn, A.M., and Clore, G.M. (1989). ``Structure determination from NMR conformational data by molecular dynamics calculations", Proceedings of the 1989 Daresbury Study Weekend. Science and engineering research council, Daresbury Laboratory, Warrington, WA4AA0, UK.

Nilges, M., Habazettl, J., Brünger, A.T., and Holak, T.A. (1991). ``Relaxation Matrix Refinement of the Solution Structure of Squash Trypsin-Inhibitor", J. Mol. Biol. 219, 499--510.

Nilges, M., Kuszewski, J., and Brünger, A.T. (1991). In: Computational Aspects of the Study of Biological Macromolecules by NMR, (J.C. Hoch, ed.). New York: Plenum Press.

Nilsson, L., Clore, G.M., Gronenborn, A.M., Brünger, A.T., and Karplus, M. (1986). ``Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: Application to 5' d(C-G-T-A-C-G)", J. Mol. Biol. 188, 455--475.

Nilsson, L. and Karplus, M. (1986). ``Empirical Energy Functions for Energy Minimization and Dynamics of Nucleic-Acids", J. Comp. Chem. 7, 591--616.

Nordman, C.E. (1980). ``Procedures for Detection and Idealization of Non-crystallographic Symmetry with Application to Phase Refinement of the Satellite Tobacco Necrocis Virus Structure", Acta Cryst. A36, 747--754.

Pearlman, D.A. and Kollman, P.A. (1991). ``Are Time-Averaged Restraints Necessary for Nuclear Magnetic Resonance Refinement? A Model Study for DNA", J. Mol. Biol. 220, 457--479.

Powell, M.J.D. (1977). ``Restart Procedures for the Conjugate Gradient Method", Mathematical Programming 12, 241--254.

Rao, S.N., Jih, J.-H., and Hartsuck, J.A. (1980). ``Rotation-Function Space Groups", Acta Cryst. A36, 878--884.

Rogers, D. (1965). ``Statistical Properties of Reciprocal Space", In "Computing Methods in Crystallography" (Rollett, J.S., ed.), 117--132.

Rossmann, M.G. and Blow, D.M. (1962). ``The Detection of Sub-Units Within the Crystallographic Asymmetric Unit", Acta Cryst. 15, 24--31.

Ryckaert, J.-P., Ciccotti, G., and Berendsen, H.J.C. (1977). ``Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes", J. Comput. Phys. 23, 327--341.

Schneider, T., Nilges, M., and Brünger, A.T. (in preparation).

Schomaker, V., Waser, J., Marsh, R.E., and Bergman, G. (1959). ``To Fit a Plane or a Line to a Set of Points by Least Squares", Acta Cryst. 12, 600--604.

Solomon, I. (1955). ``Relaxation Processes in a System of 2 Spins", Phys. Rev. 99, 559--565.

Stout, G.H. and Jensen, L.H. (1989). X-ray Structure Determination, Wiley, New York.

Strong, R., (1990). Ph.D. diss., Harvard University.

Tarjan, R. (1983). Data Structures and Network Algorithms. Society for Industrial and Applied Mathematics, Philadelphia.

Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1989) ``Time-Dependent Distances Restraints in Molecular Dynamics Simulations", Chem. Phys. Letters 157, 289--294.

Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1990) ``Time-Averaged Nuclear Overhauser Effect Distance Restraints Applied to Tendamistat", J. Mol. Biol. 214, 223--235.

Treutlein, H., Schulten, K., Deisenhofer, J., Michel, H., Brünger, A.T., and Karplus, M. (1992). ``Chromophore-Protein Interactions and the Function of the Photosynthetic Reaction Center: A Molecular Dynamics Study", Proc. Natl. Acad. Sci. USA 89, 75--79.

Verlet, L. (1967). ``Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules", Phys. Rev. 159, 98--105.

Weiner, S., Kollman, P., Case, D., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., and Weiner, P. (1984). ``A new force field for molecular mechanical simulation of nucleic acids and proteins", J. Am. Chem. Soc. 106, 765--784.

Weis, W. I., Brünger, A. T., Skehel, J. J., and Wiley, D. C. (1990). ``Refinement of the Influenza Virus Haemagglutinin by Simulated Annealing", J. Mol. Biol. 212, 737--761.

Wilson, A.J.C. (1949). ``The Probability Distribution of X-ray Intensities", Acta Cryst. 2, 318--321.

Wolfram, S. (1991). Mathematica, A System for Doing Mathematics by Computer, 2nd Ed. Redwood City, California: Addison-Wesley Publishing Company, Inc.

Yip, P. and Case, D. A. (1989). ``A New Method for Refinement of Macromolecular Structures based on Nuclear Overhauser Effect Spectra", J. Magn. Reson. 83, 643--648.



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