Abad-Zapatero, C., J. P. Griffith, J. L. Sussman & M. G. Rossman (1987). Refined Crystal Structure of Dogfish M4 Apo-lactate Dehydrogenase. J. Mol. Biol. 198, 445-67.

Adams, M. J., G. C. Ford, R. Koekoek, P. J. J. Lentz, A. J. McPherson, M. G. Rossman, I. E. Smiley, I. E. Schevitz & A. J. Wonacott (1970). The Structure of Lactate Dehydrogenase at 2.8 Å Resolution. Nature 227, 1098-1103.

Adams, M. J., A. Liljas & M. G. Rossman (1973). J. Mol. Biol. 76, 519-31.

Adobe Systems Incorporated (1985). Postscript Language Reference Manual. Reading, MA: Addison-Wesley.

Ahlström, P., O. Teleman & B. Jönsson (1988). Molecular Dynamics Simulation of Interfacial Water Structure and Dynamics in a Parvalbumin Solution. J. Am. Chem. Soc. 110, 4198-4203.

Ahlström, P., O. Teleman, J. Kördel, S. Forsén & B. Jönsson (1989). A Molecular Dynamics Simulation of Bovine Calbindin D9k. Molecular Structure and Dynamics. Biochemistry 28, 3205-3211.

Aisen, I. & I. Listowsky (1980). Ann. Rev. Biochem. 49, 357-393.

Alber, T., D. W. Banner, A. C. Bloomer, G. A. Petsko, D. Phillips, P. S. Rivers & I. A. Wilson (1981). On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. Phil. Trans. R. Soc. Lond. B293, 159-171.

Allen, M. P. & D. J. Tildesley (1987). Computer Simulation of Liquids. Oxford: Clarendon Press.

Alliant Computer (1991). A Tuning Guide: User Experiences with Alliant FX/Fortran-2800. Alliant Technical Reports. 91-001.

Amit, A. G., R. A. Mariuzza, S. E. V. Phillips & R. J. Poljak (1986). Three dimensional structure of an antigen-antibody complex at 2.8 Å resolution. Science 233, 747-753.

Anderson, B. F., H. M. Baker, E. J. Dodson, G. E. Norris, S. V. Rumball, J. M. Waters & E. N. Baker (1987). Structure of Human Lactoferrin at 3.2 Å Resolution. Proc. Natl. Acad. Sci. USA 84, 1769-1773.

Anderson, B. F., H. M. Baker, G. E. Norris, D. W. Rice & E. N. Baker (1989). Structure of Human Lactoferrin: Crystallographic Structure Analysis and Refinement at 2.8 Å Resolution. J. Mol. Biol. 209, 711-734.

Anderson, B. F., H. M. Baker, G. E. Norris, S. V. Rumball & E. N. Baker (1990). Apolactoferrin structure demonstrates ligand-induced conformational change in transferrins. Nature 344, 784-787.

Anderson, C. M., R. E. Stenkamp & T. A. Steitz (1978). Sequencing a protein by x-ray crystallography. ii. Refinement of yeast hexokinase B co-ordinates and sequence at 2.1 Angstroms resolution. J. Mol. Biol. 123, 15.

Anderson, C. M., F. H. Zucker & T. Steitz (1979). Space-filling models of kinase clefts and conformation changes. Science 204, 375-380.

Aqvist, J. & O. Tapia (1987). Surface fractality as a guide for studying protein-protein interactions. J. Mol. Graph. 5, 31-34.

Arnott, S. & S. D. Dover (1967). J. Mol. Biol. 30, 209-212.

Avbelj, F., J. Moult, D. H. Kitson, M. N. G. James & A. T. Hagler (1990). Molecular Dynamics Study of the Structure and Dynamics of a Protein Molecule in a Crystalline Ionic Environment, Streptomyces griseus Protease A. Biochemistry 29, 8658-8676.

Baker, E. N., B. F. Anderson, H. M. Baker, M. Haridas, G. B. Jameson, G. E. Norris, S. V. Rumball & C. A. Smith (1991). Structure, Function and Flexibility of Human Lactoferrin. Int. J. Biol. Macromol. 13, 122-129.

Baker, E. N. & R. E. Hubbard (1984). Hydrogen Bonding in Globular Proteins. Prog. Biophys. Mol. Biol. 44, 97-179.

Baker, E. N., S. V. Rumball & B. F. Anderson (1987). Transferrins: insights into structure and function from studies on lactoferrin. Trends Biochem. Sci. 12, 350-253.

Banner, D. W., A. C. Bloomer, G. A. Petsko, D. C. Phillips, C. I. Pogson, I. A. Wilson, P. H. Conan, A. J. Furth, J. D. Milmar, R. E. Offord, J. D. Priddle & S. G. Waley (1975). Structure of chicken muscle triosephosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data. Nature 255, 609-614.

Ben-Naim, A. (1980). Hydrophobic Interactions. New York: Plenum Press.

Bennett, W. S. & R. Huber (1984). Structural and Functional Aspects of Domain Motion in Proteins. Crit. Rev. Biochem 15, 291-384.

Bennett, W. S., Jr & T. A. Steitz (1980a). Structure of a complex between yeast hexokinase A and glucose. I. Structure determination and refinement at 3.5 Å resolution. J. Mol. Biol. 140, 183-211.

Bennett, W. S., Jr & T. A. Steitz (1980b). Structure of a complex between hexokinase A and glucose: II. Detailed comparisons of conformation and active site configuration with the native hexokinase B monomer and dimer. J. Mol. Biol. 140, 211-230.

Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer Jr, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi & M. Tasumi (1977). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.

Bhat, T., E. Padlan & D. Davies (1992). Refined crystal structure of the galactan-binding immunoglobulin Fab J539 at 1.95 Å resolution. Personal Communication.

Birktoft, J. J., R. T. Fernley, R. A. Bradshaw & L. J. Banaszak (1982). Amino acid sequence homology among the 2-hydroxy acid dehydrogenases: Mitochondrial and cytoplasmic malate dehydrogenases form a homologous system with lacate dehydrogenase. Proc. Nat. Acad. Sci. USA 79, 6166-70.

Branden, C. & J. Tooze (1991). Introduction to Protein Structure. New York: Garland Publishing Incorporated.

Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Cryst. A32, 832-847.

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

Brooks, C. L. I. & M. Karplus (1986). Theoretical Approaches to Solvation of Biopolymers. Meth. Enzym. 127, 369-400.

Brown, F. K. & P. A. Kollman (1987). Molecular Dynamics Simulation of ‘Loop Closing’ in the Enzyme Triose Phosphate Isomerase. J. Mol. Biol. 198, 533-46.

Bruccoleri, R. E., E. Haber & J. Novotny (1988). Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature 335, 564-568.

Bruccoleri, R. E. & M. Karplus (1987). Biopolymers 26, 137-168.

Bruccoleri, R. E., M. Karplus & J. A. McCammon (1986). The Hinge-Bending Mode of a Lysozyme Inhibitor Complex. Biopolymers 25, 1767-1802.

Brünger, A. T. (1990). X-PLOR 2.1 manual. New Haven: Yale University.

Brünger, A. T., J. Kuriyan & M. Karplus (1987). Crystallographic R factor refinement by molecular dynamics. Science 235, 458-60.

Carbo, R., L. Leyda & M. Arnau (1980). Int. J. Quantum Chem. 17,

Carriero, N. & D. Gelernter (1989). Linda in Context. Communications of the ACM 32, 444-458.

CCP4 (1991). The Cooperative Computing Project 4: Protein Crystallography. Warrington, England: SERC Daresbury Laboratory.

Chandler, D. & H. C. Andersen (1972). Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids. J. Chem. Phys. 57, 1930-1937.

Chandler, D. & C. S. Hsu (1977). Comparisons of Monte Carlo and RISM calculations of pair correlation functions. J. Chem. Phys. 66, 5231-5234.

Chandler, D., J. D. Weeks & H. C. Andersen (1983). Van der Waals Picture of Liquids, Solids, and Phase-transformations. Science 220, 787-794.

Cheng, X. & B. Schoenborn (1990). Hydration in Protein Crystals: A Neutron Diffraction Analysis of Carbonmonoxymyoglobin. Acta Cryst. B46, 195-208.

Cheng, X. & B. P. Sehoenborn (1991). Neutron Diffraction Study of Carbonmonoxymyoglobin. J. Mol. Biol. 220, 381-399.

Cherfils, J., S. Duquerroy & J. Janin (1991). Protein-protein Recognition Analyzed by Docking Simulation. Proteins: Struct. Func. Genet. 11, 271-80.

Chothia, C. (1974). Hydrophobic bonding and accessible surface area in proteins. Nature 248, 338-339.

Chothia, C. (1975). Structural invariants in protein folding. Nature 254, 304-308.

Chothia, C. (1984). Principles that determine the structure of proteins. Ann. Rev. Biochem. 53, 537-72.

Chothia, C. (1992). Proteins — 1000 families for the molecular biologist. Nature 357, 543-544.

Chothia, C. & A. V. Finkelstein (1990). The classification and origins of protein folding patterns. Ann. Rev. Biochem. 59, 1007-39.

Chothia, C. & A. M. Lesk (1985). Helix movements in proteins. Trends Biochem. Sci. 10, 116-118.

Chothia, C. & A. M. Lesk (1987). Canonical structures for the hypervariable regions of the immunoglobulins. J. Mol. Biol. 196, 901-917.

Chothia, C., A. M. Lesk, G. G. Dodson & D. C. Hodgkin (1983). Transmission of conformational change in insulin. Nature 302, 500-505.

Chothia, C., A. M. Lesk, A. Tramontano, M. Levitt, S. J. Smith- Gill, G. Air, S. Sheriff, E. A. Padlan, D. Davies, W. R. Tulip, P. M. Colman, S. Spinelli, P. M. Alzari & R. J. Poljak (1989). Conformations of the immunoglobulin hypervariable regions. Nature 342, 877-883.

Chothia, C., M. Levitt & D. Richardson (1981). Helix to helix packing in proteins. J. Mol. Biol. 145, 215-250.

Clarke, A. R., D. B. Wigley, W. N. Chia, D. Barstow, T. Atkinson & J. J. Holbrook (1986). Site-directed mutagenesis reveals role of mobile arginine residue in lactate dehydrogenase catalysis. Nature 324, 699-702.

Colonna-Cesari, F., D. Perahia, M. Karplus, H. Eklund, C. I. Branden & O. Tapia (1986). Interdomain motion in liver alcohol dehydrogenase: structural and energetic analysis of the hinge bending mode. J. Biol. Chem. 261, 15273-15280.

Connolly, M. (1983a). Analytical Molecular Surface Calculation. J. Appl. Cryst. 16, 548-558.

Connolly, M. (1983b). Solvent-accessible Surfaces of Proteins and Nucleic Acids. Science 221, 709-713.

Connolly, M. (1986). Measurement of protein surface shape by solid angles. J. Mol. Graph. 4, 3-6.

Connolly, M. L. (1981). The MS program. QCPE Bull. 1, 75.

Creighton, T. E. (1984). Proteins. San Francisco: Freeman.

Cybulski, S. & S. Scheiner (1989). J. Phys. Chem. 93, 6565.

Daggett, V., P. A. Kollman & I. D. Kuntz (1991). A Molecular-dynamics Simulation of Polyalanine - an Analysis of Equilibrium Motions and Helix-Coil Transitions. Biopolymers 31, 1115-1134.

Daggett, V. & M. Levitt (1992). Molecular-dynamics Simulations of Helix Denaturation. J. Mol. Biol. 223, 1121-1138.

Davenport, R. C., P. A. Bash, B. A. Seaton, M. Karplus, G. A. Petsko & D. Ringe (1991). Structure of the triosephosphate isomerase-phosphoglycolohydroxyamate complex: an analogue of the intermediate in the reaction pathway. Biochemistry 30, 5821-5826.

Dayringer, H. E., A. Tramontano, S. R. Sprang & R. J. Fletterick (1986). Interactive program for visualization and modelling of proteins, nucleic acids and small molecules. J. Mol. Graph. 4, 82-87.

Dean, P. M. & P. L. Chau (1987). Molecular recognition: optimized searching through rotational 3-space for pattern matches on molecular surfaces. J. Mol. Graphics 5, 152-164.

Diamond, B. (1971). A real-space refinement procedure for proteins. Acta Cryst. A27, 436-52.

Diamond, R. (1976). On the comparison of conformations using linear and quadratic transformations. Acta Cryst. A32, 1-10.

Diamond, R. (1988). A note on the rotational superposition problem. Acta Cryst. A44, 211-6.

Diamond, R. (1989). A comparison of three recently published methods for superimposing vector sets by pure rotation. Acta Cryst. A45, 657.

Diamond, R. (1990). On the factorization of rotations with examples in diffractometry. Proc. R. Soc. Lond. A428, 451-472.

Diamond, R. D. (1992). On the Multiple Simultaneous Superposition of Coordinate Sets by Rigid-Body Transformations. Protein Science (in press)

Dickerson, R. E. & I. Geis (1969). The Structure and Action of Proteins. New York: Harper & Row

Diederichs, K. & G. E. Schulz (1990). Three-dimensional structure of the complex between mitochondrial matrix adenylate kinase and its substrate AMP. Biochemistry 29, 8138-8144.

Diederichs, K. & G. E. Schulz (1991). Refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution. J. Mol. Biol. 217, 541-549.

Dill, K. A. (1990). Dominant Forces in Protein Folding. Biochemistry 29, 7133-7155.

Dreusicke, D. & G. E. Schulz (1988). The switch between two conformations of adenylate kinase. J. Mol. Biol. 203, 1021-1028.

Duquerroy, S., J. Cherfils & J. Janin (1991). Protein-protein interaction: an analysis by computer simulation. Ciba Found. Symp. 161, 237-49.

Eisenberg, D. & W. Kauzmann (1969). The Structure and Properties of Water. Oxford: Clarendon Press.

Eisenberg, D. & A. D. McLachlan (1987). Solvation energy in protein folding and binding. Nature 319, 199-203.

Eklund, H., J. P. Samaha, L. Wallen, C. I. Branden, A. Akeson & T. A. Jones (1981). Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution. J. Mol. Biol. 146, 561-587.

Eklund, H., J. P. Samama & T. A. Jones (1984). Crystallographic investigations of nicotinamide adenine dinucleotide binding to horse liver alcohol dehydrogenase. Biochemisty 23,

Elber, R. & M. Karplus (1987). Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235, 318-321.

Epp, O., E. Latham, M. Schiffer, R. Huber & W. Palm (1975). Biochemistry 14, 4943-52.

Faber, H. R. & B. W. Matthews (1990). A mutant T4 lysozyme displays five different crystal conformations. Nature 348, 263-266.

Finney, J. L. (1978). Volume Occupation, Environment, and Accessibility in Proteins. Environment and Molecular Area of RNase-S. J. Mol. Biol. 119, 415-441.

Finney, J. L., J. E. Quinn & J. O. Baum (1985). The Water Dimer Potential. Water Science Reviews 1, 93-170.

Flaherty, K. M., C. R. de Luca-flaherty & D. B. McKay (1990). Three-dimensional structure of the ATPase fragment of a 70kd heat-shock cognate protein. Nature 346,

Forester, T. R. & I. R. McDonald (1991). Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA. Mol. Phys. 72, 643-660.

Franks, F. (Ed.) (1973). Water: A Comprehensive Treatise. New York: Plenum Press.

Franks, F. (1982). Hydrophobic Interactions - a Historical Perspective. Faraday Symp. Chem. Soc. 17, 7-10.

Franks, F. (1983). Water. London: The Royal Society of Chemistry.

Frauenfelder, H., S. G. Sligar & P. G. Wolynes (1991). The Energy Landscapes and Motions of Proteins. Science 254, 1598-1603.

Geiger, A., A. Rahman & F. H. Stillinger (1979). J. Chem. Phys. 70, 273-6.

Gelernter, D. (1987). Programming for Advanced Computing. Scientific American 257, 90-98.

Gill, S. J., S. F. Dec, G. Olofsson & I. Wadsö (1985). Anomalous Heat Capacity of Hydrophobic Solvation. J. Phys. Chem. 89, 3758-3761.

Gilliland, G. L. & F. A. Quiocho (1981). Structure of the L-Arabinose-Binding Protein from Escherichia coli at 2.4 Å Resolution. J. Mol. Biol. 146, 341.

Goldstein, H. (1980). Classical Mechanics. 2nd edition. New York: Addison-Wesley.

Goodfellow, J., N. Thanki & J. M. Thorton (1989). Preliminary analysis of water molecule distributions in proteins. Mol. Sim. 3, 167-182.

Grau, U. M., W. E. Trommer & M. G. Rossman (1981). Structure of the Active Ternary Complex of Pig Heart Lactate Dehydrogenase with S-lac-NAD at 2.7 Å Resolution. J. Mol. Biol. 151, 289-307.

Gray, C. G. & K. E. Gubbins (1984). Theory of molecular fluids I: Fundamentals. Oxford: Clarendon Press.

Greer, J. & B. L. Bush (1978). Macromolecular Shape and Surface Maps by Solvent Exclusion. Proc. Natl. Acad. Sci. USA 75, 303-7.

Guldbrand, L., T. R. Forester & R. M. Lynden-Bell (1989). Distribution and dynamics of mobile ions in systems of ordered B-DNA. Mol. Phys. 67, 473-93.

Hagler, A. T. & J. Moult (1978). Computer simulation of the solvent structure around biological macromolecules. Nature 272, 222-226.

Hagler, A. T., D. J. Osguthorpe & B. Robson (1980). Monte Carlo Simulation of Water Behavior Around the Dipeptide N-Acetylalanyl-N-Methylamide. Science 208, 599-601.

Halle, B., T. Andersson, S. Forsén & B. Lindman (1981). Protein Hydration from Water Oxygen-17 Magnetic Relaxation. J. Am. Chem. Soc. 1981, 500-508.

Hansen, J. P. & I. R. McDonald (1986). Theory of Simple Liquids. Boston: Academic Press.

Harbison, S. P. & G. L. Steele Jr (1987). C: A Reference Manual. 2nd edition. Englewood, NJ: Prentice-Hall.

Herron, J. N., X. He, M. L. Mason, E. W. Voss & A. B. Edmundson (1989). Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentandiol. Proteins 5, 271-280.

Hirata, F. & P. J. Rossky (1981). J. Chem. Phys. 74, 6867.

Hirshberg, M. (1990). Simulations of the Static and Dynamic Properties of the DNA Double Helix. Weizmann Institute of Science.

Hodgkin, E. E. & W. G. Richards (1987). Int. J. Quantum Chem. Quantum Biol. Symp. 14, 105.

Holbrook, J. J. & H. Gutfreund (1973). Approaches to the Study of Enzyme Mechanisms: Lactate Dehydrogenase. FEBS Letters 31, 157-169.

Holbrook, J. J., A. Liljas, S. J. Steindel & M. G. Rossman (1975). New York: Academic Press.

Hvidt, A. (1983). The interaction of water with nonpolar solutes. Ann. Rev. Biophys. Bioeng. 12, 1-20.

Islam, S. A. & D. L. Weaver (1991). Variation of Folded Polypeptide Size with Probe Size. Proteins: Struct. Func. Genet. 10, 300-314.

Janin, J. & C. Chothia (1990). The Structure of Protein-protein Recognition Sites. J. Biol. Chem. 265, 16027-16030.

Janin, J., S. Miller & C. Chothia (1988). Surface, Subunit Interfaces and Interior of Oligomeric Proteins. J. Mol. Biol. 204, 155-64.

Janin, J. & S. Wodak (1983). Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol. 42, 21-78.

Jiang, F. & S.-H. Kim (1991). ‘Soft-docking’: Matching of molecular surface cubes. J. Mol. Biol. 219, 79-102.

Jones, T. A. (1982). in Computational Crystallography. (ed. Sayre, D.) Oxford: Claredon Press.

Jones, T. A. (1985). Interactive Computer Graphics: FRODO. Meth. Enzym. 115, 157-171.

Jones, T. A., J. Y. Zou, S. W. Cowan & M. Kjeldgaard (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110-9.

Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey & M. L. Klein (1983). Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 79, 926-935.

Joseph, D., G. A. Petsko & M. Karplus (1990). Anatomy of Conformational Change: Hinged ‘Lid’ Motion of the Triosephosphosphate Isomerase Loop. Science 249, 1425-1428.

Kabsch, W., H. G. Mannherz, D. Suck, E. F. Pai & K. C. Holmes (1990). Atomic structure of the actin-DNase I complex. Nature 347, 37-44.

Kearsley, S. K. (1989). Structural comparisons using restrained inhomogeneous transformations. Acta Cryst. A45, 628-35.

Kearsley, S. K. (1990b). An algorithm for the simultaneous superposition of a structural series. J. Comp. Chem. 11, 1187-92.

Kernigan, B. W. & R. Pike (1984). The Unix Programming Environment. Englewood Cliffs, NJ: Prentice-Hall.

Kim, P. S. & R. L. Baldwin (1990). Intermediates in the folding reactions of small proteins. Ann. Rev. Biochem. 59, 631-660.

Kincaid, R. H. & H. A. Scheraga (1982). Acceleration of Convergence in Monte Carlo Simulations of Aqueous Solutions Using the Metropolis Algorithm. Hydrophobic Hydration of Methane. J. Comp. Chem. 3, 525-547.

Knowles, J. R. (1991). To build an enzyme... Phil. Trans. R. Soc. Lond. B 332, 115-121.

Kossiakoff, A. A. (1985). The Application of Neutron Crystallography to the Study of Dynamic and Hydration Properties of Proteins. Ann. Rev. Biochem. 54, 1195-227.

Kraulis, P. J. (1991). MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.

Kuntz, I. D. (1992). Structure-Based Strategies for Drug Design and Discovery. Science 257, 1078-1082.

Kuntz, I. D., J. M. Blaney, S. J. Oatley, R. Langridge & T. E. Ferrin (1982). A Geometric Approach to Macromolecule Ligand Interaction. J. Mol. Biol. 161, 269-288.

Laaksonen, A., L. G. Nilsson, B. Jönsson & O. Teleman (1989). Molecular-dynamics Simulation of Double Helix Z-DNA in Solution. Chem. Phys. 129, 175.

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

Lee, C. Y., J. A. McCammon & P. J. Rossky (1984). The structure of liquid water at an extended hydrophobic surface. J. Chem. Phys. 80, 4448-4455.

Leicester, S. E., J. L. Finney & R. P. Bywater (1988). Description of molecular surface shape using Fourier descriptors. J. Mol. Graphics 6, 104-108.

Lesk, A. M. (1986a). in Computer Applications in the Biosciences. (ed. Saccone, C.) Brussels: EEC.

Lesk, A. M. (1986b). A toolkit for computational molecular biology. II. On the optimal superposition of two sets of coordinates. Acta Cryst. A42, 110-3.

Lesk, A. M. (1991). Protein Architecture: A Practical Approach. Oxford: IRL Press.

Lesk, A. M. & C. Chothia (1984). Mechanisms of Domain Closure in Proteins. J. Mol. Biol. 174, 175-91.

Lesk, A. M. & C. Chothia (1988). Elbow Motion in the immunoglobins involves a molecular ball and socket joint. Nature 335, 188-190.

Lesk, A. M. & C. H. Chothia (1980). How Different Amino Acid Sequences Determine Similar Protein Structures: The Structure and Evolutionary Dynamics of the Globins. J. Mol. Biol. 136, 225-270.

Lesk, A. M. & K. D. Hardmann (1982). Computer-generated schematic diagrams of protein structures. Science 216, 539-40.

Leslie, A. G. W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of B C Wang. Acta Cryst. A43, 134-136.

Levitt, M. (1989). Molecular dynamics of macromolecules in water. Chemica Scripta 29A, 197-203.

Levitt, M. (1991). Real-Time Interactive Frequency Filtering of Molecular-Dynamics Trajectories. J. Mol. Biol. 220, 1-4.

Levitt, M. & C. Chothia (1976). Structural patterns in globular proteins. Nature 261, 552-558.

Levitt, M., C. Sander & P. S. Stern (1985). Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease, and lysozyme. J. Mol. Biol. 181, 423-447.

Levitt, M. & R. Sharon (1988). Accurate Simulation of Protein Dynamics in Solution. Proc. Natl. Acad. Sci. USA 85, 7557-7561.

Lewis, M. & D. C. Rees (1985). Fractal surfaces of proteins. Science 230, 1163-65.

Lolis, E., T. Alber, R. C. Davenport, D. Rose, F. C. Hartmann & G. A. Petsko (1990). Structure of yeast triosephosphate isomerase at 1.9 Å resolution. Biochemistry 29, 6609-6618.

Louie, G. V., P. D. Brownlie, R. Lambert, J. B. Cooper, T. L. Blundell, S. P. Wood, M. J. Warren, S. C. Woodcock & P. M. Jordan (1992). Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site. Nature 359, 33-39.

Luecke, H. & F. A. Quiocho (1990). High specificity of a phosphate-transport protein determined by hydrogen-bonds. Nature 347, 402-406.

Mao, B. & J. A. McCammon (1983). Theoretical Study of Hinge Bending in L-Arabinose-binding Protein. J. Biol. Chem. 258, 12543-12547.

Mao, B. & J. A. McCammon (1984). Structural Study of Hinge Bending in L-Arabinose-binding Protein. J. Biol. Chem. 259, 4964-70.

Mao, B., M. R. Pear & J. A. McCammon (1982). Hinge-bending in L-Arabinose-binding Protein. J. Biol. Chem. 257, 1131-1133.

Marquart, M., J. Deisenhofer, R. Huber & W. Palm (1980). Crystallographic Refinement and atomic models of the intact immunoglobulin molecule KOL and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution. J. Mol. Biol. 141, 369.

Martin, A. C. R., J. C. Cheetham & A. R. Rees (1989). Modeling antibody hypervariable loops: A combined algorithm. Proc. Nat. Acad. Sci. USA 86, 9268-9272.

Max, N. L. (1984). Computer representation of molecular surfaces. J. Mol. Graphics 2, 8-13.

Max, N. L. & E. D. Getzoff (1988). Spherical harmonic molecular surfaces. IEEE Comp. Graphics and Applications 8, 42-50.

McLachlan, A. D. (1972). A mathematical procedure for superimposing atomic coordinates of proteins. Acta Cryst. A28, 656-7.

McLachlan, A. D. (1979). Rapid comparision of protein structures. Acta Cryst. A38, 871-3.

McPhalen, C. A., M. G. Vincent & J. N. Jansonius (1992a). X-ray structure refinement and comparison of 3 forms of mitochondrial aspartate-aminotransferase. J. Mol. Biol. 225, 495-517.

McPhalen, C. A., M. G. Vincent, D. Picot, J. N. Jansonius, A. M. Lesk & C. Chothia (1992b). Domain closure in mitochondrial aspartate aminotransferase. J. Mol. Biol. 227, 197-213.

Mehrotra, P. K., F. T. Marchese & D. L. Beveridge (1981). Statistical State Solvation Sites. J. Am. Chem. Soc. 103, 672-3.

Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. Teller & E. Teller (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-92.

Metropolis, N. & S. Ulam (1949). The Monte-Carlo Method. J. Am. Stat. Ass. 44, 335-341.

Mezei, M. & D. L. Beveridge (1986). Structural Chemistry of Biomolecular Hydration via Computer Simulation: The Proximity Criteria. Meth. Enzym. 127, 21-47.

Miller, M., J. Schneider, B. K. Sathyanarayana, M. V. Toth, G. R. Marshall, L. Clawson, L. Selk, S. B. H. Kent & A. Wlodawer (1989). Structure of Complex of Synthetic HIV-1 Protease with a Substrate-Based Inhibitor at 2.3 Å Resolution. Science 246, 1149-52.

Miller, S., J. Janin, A. M. Lesk & C. Chothia (1987a). Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-56.

Miller, S., A. M. Lesk, J. Janin & C. Chothia (1987b). The accessible surface area and stability of oligomeric proteins. Nature 328, 834-6.

Milstein, C. (1990). Antibodies: a paradigm for the biology of molecular recognition. Proc. R. Soc. (London) B239:1-16,

Mowbray, S. L. (1992). Ribose and glucose-galactose receptors. Competitors in bacterial chemotaxis. J. Mol. Biol. 227, 418-440.

Muirhead, H., J. M. Cox, C. Mazzarella & M. F. Perutz (1967). Structure and function of haemoglobin III. A three-dimensional fourier synthesis of human deoxyhaemoglobin at 5.5 Å resolution. J. Mol. Biol. 28, 117-156.

Müller, C. W. & G. E. Schulz (1988). Structure of the complex of adenylate kinase from Escherichia coli and the inhibitor P1, P5-di(adenosine-5'-) pentaphosphate. J. Mol. Biol. 202, 909-912.

Müller, C. W. & G. E. Schulz (1992). Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution. J. Mol. Biol. 224, 159-177.

Musick, W. D. L. & M. G. Rossman (1979). The Structure of Mouse Testicular Lactate Dehydrogenase Isoenzyme C4 at 2.9 Å Resolution. J. Biol. Chem. 254, 7611-7620.

Namasivayam & P. M. Dean (1986). Statistical method for surface pattern-matching between dissimilar molecules: electrostatic potentials and accessible surfaces. J. Mol. Graphics 4, 46-50.

Nicolls, A., K. A. Sharp & B. Honig (1991). Protein Folding and Association: Insights from the Interfacial and Thermodynamic Properties of Hydrocarbons. Proteins: Struc. Func. Genet. 11, 281-296.

Noble, M. E. M., R. K. Wirenga, A. M. Lambeir, F. R. Opperdoes, A. M. W. H. Thunnissen, K. H. Kalk, H. Groendijk & W. G. J. Hol (1991). The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes. Proteins: Struc. Func. Genet. 10, 50-69.

Norris, G. E., B. F. Anderson & E. N. Baker (1991). Molecular Replacement Solution of the Structure of Apolactoferrin, A Protein Displaying Large-Scale Conformational Change. Acta Cryst. B47, 998-1004.

Otting, G., E. Liepinsh & K. Wüthrich (1991). Protein Hydration in Aequous Solution. Science 254, 974-80.

Owicki, J. C. & H. A. Scheraga (1977). J. Am. Chem. Soc. 99, 7413.

Padlan, E. A., E. W. Silverton, S. Sheriff, G. H. Cohen, G. S. Smith-Gill & D. R. Davies (1989). Proc. Natl. Acad. Sci. USA 86, 5938-5942.

Pangali, C., M. Rao & B. J. Berne (1979). Hydrophobic hydration around a pair of apolar species in water. J. Chem. Phys. 71, 2975-2981.

Parker, D. M., D. Jeckel & J. J. Holbrook (1982). Slow structural changes shown by the 3-nitrotyrosine-237 residue in pig heart [Tyr(3NO2)237] lactate dehydrogenase. Biochem. J. 201, 465-471.

Perutz, M. (1989). Mechanisms of cooperativity and allosteric regulation in proteins. Quart. Rev. Biophys. 22, 139-236.

Pfeifer, P., U. Welz & H. Wipperman (1985). Factal surface dimension of proteins: lysozyme. Chem. Phys. Lett. 113, 535-40.

Pflugrath, J. W. & F. A. Quiocho (1988). The 2 Å Resolution Structure of the Sulfate-binding Protein Involved in Active-transport in Salmonella typimurium. J. Mol. Biol. 200, 163-180.

Phillips, D. C., P. S. Rivers, M. J. E. Sternberg, J. M. Thornton & I. A. Wilson (1977). Biochem. Soc. Trans. 5, 642-647.

Ponder, J. W. & F. M. Richards (1987). Tertiary templates for proteins: use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193, 775-791.

Pratt, L. R. & D. Chandler (1977). Theory of the hydrophobic effect. J. Chem. Phys. 67, 3683-3704.

Press, W. H., B. P. Flannery, S. A. Teukolsky & W. T. Vetterling (1988). Numerical Recipes in C. Cambridge: Cambridge University Press.

Ptitsyn, O. B. (1987). Protein Folding: Hypotheses and Experiment. J. Protein Chem. 6, 272-93.

Quiocho, F. A. (1990). Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria. Phil. Trans. Roy. Soc. Lond. B326, 341-351.

Raghavan, K., K. Foster & M. Berkowitz (1991). Comparison of the structure and dynamics of water at the Pt(111) and Pt(100) interfaces: molecular dynamics study. Chem. Phys. Lett. 177, 426-32.

Rapaport, D. C. & H. A. Scheraga (1982). Hydration of Inert Solutes. A Molecular Dynamics Study. J. Phys. Chem. 86, 873-880.

Rau, D. C., B. Lee & V. A. Parsegian (1984). Measurement of the repulsive force between poly-electrolyte molecules in ionic solution — hydration forces between parallel DNA double helices. Proc. Natl. Acad. Sci. USA 81, 2621-2625.

Rau, D. C. & V. A. Parsegian (1992). Direct measurement of the intermolecular forces between counterion-condensed DNA double helices — evidence for long-range attractive hydration forces. Biophys. J. 61, 246-259.

Remington, S., G. Wiegand & R. Huber (1982). Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 Å resolution. J. Mol. Biol. 158, 111-152.

Richards, F. M. (1974). The Interpretation of Protein Structures: Total Volume, Group Volume Distributions and Packing Density. J. Mol. Biol. 82, 1-14.

Richards, F. M. (1977). Areas, Volumes, Packing, and Protein Structure. Ann. Rev. Biophys. Bioeng. 6, 151-76.

Richards, F. M. (1979). Packing Defects, Cavities, Volume Fluctuations, and Access to the Interior of Proteins. Including Some General Comments on Surface Area and Protein Structure. Carlsberg. Res. Commun. 44, 47-63.

Richmond, T. J. (1984). Solvent Accessible Surface Area and Excluded Volume in Proteins: Analytical Equations for Overlapping Spheres and Implications for the Hydrophobic Effect. J. Mol. Biol. 178, 63-89.

Rini, J. M., U. Schulze-Gahmen & I. A. Wilson (1992). Structural Evidence for Induced-fit as a Mechanism for Antibody-antigen Recognition. Science 255, 959-965.

Rojewska, D. & R. Elber (1990). Molecular dynamics study of secondary structure motions in proteins: application to myohemerythrin. Proteins 7, 265-279.

Rosenfeld, A. & A. C. Kak (1982). Digital Picture Processing. New York: Academic Press.

Rossky, P. J. & M. Karplus (1979). Solvation. A Molecular Dynamics Study of a Dipeptide in Water. J. Am. Chem. Soc. 101, 1913.

Rossmann, M. G., M. J. Adams, M. Buehner, G. C. Ford, M. L. Hackert, P. J. Lentz Jr, A. McPherson Jr, R. W. Schevitz & I. E. Smiley (1971). Cold Spring Harbor Symp. Quant. Biol. 36,

Rossmann, M. G., A. Liljas, C. I. Branden & L. J. Banaszak (1975). New York: Academic Press.

Sack, J. S., S. D. Trakhanov, I. H. Tsigannik & F. A. Quiocho (1989). Structure of the L-Leucine-binding Protein Refined at 2.4 Å Resolution and Comparison with the Leu/Ile/Val-binding Protein Structure. J. Mol. Biol. 206, 193-207.

Saenger, W. (1987). Structure and Dynamics of Water Surrounding Biomolecules. Ann. Rev. Biophys. Biophys. Chem. 16, 93-114.

Sampson, N. S. & J. R. Knowles (1992a). Segmental Movement: Definition of the Structural Requirements for Loop Closure in Catalysis by Triosphosphate Isomerase. Biochemistry 31, 8482-8487.

Sampson, N. S. & J. R. Knowles (1992b). Segmental Motion in Catalysis: Investigation of a Hydrogen Bond Critical for Loop Closure in the Reaction of Triosephosphate Isomerase. Biochemistry 31, 8488-8494.

Sarra, R., R. Garratt, B. Gorinsky, H. Jhoti & P. Lindlay (1990). High-resolution X-ray studies on rabbit serum transferrin — preliminary structure analysis of the N-terminal half-molecule at 2.3 Å resolution. Acta Cryst. B46, 763-771.

Satow, Y., G. H. Cohen, E. A. Padlan & D. R. Davies (1986). Phosphocholine binding immunoglobulin Fab McPC603: An X-ray diffraction study at 2.7 Å. J. Mol. Biol. 190, 593-604.

Schlenkrich, M., K. Nicklas, J. Brickmann & P. Bopp (1990). A molecular dynamics study of the interface between a membrane and water. Ber. Bunsenges. Phys. Chem. 94, 133-145.

Schulz, G. E. (1992). Induced-fit movements in adenylate kinases. Faraday Discuss. 93, 000-000.

Schulz, G. E., M. Elzinga, F. Marx & R. H. Schirmer (1974). Three-dimensional structure of adenylate kinase. Nature 250, 120-123.

Schulz, G. E., C. W. Muller & K. Diederichs (1990). Induced-fit movement in adenylate kinases. J. Mol. Biol. 213, 627-630.

Schulze-Gahmen, U., J. M. Rini, J. Arevalo, E. A. Stura, J. H. Kenten & I. A. Wilson (1988). Preliminary crystallographic data, primary sequence, and binding data for an anti-peptide Fab and its complex with a synthetic peptide from influenza virus hemagglutinin. J. Biol. Chem. 263, 17100-17105.

Sciortino, F., A. Geiger & H. E. Stanley (1991). Effect of defects on molecular mobility in liquid water. Nature 354, 218-221.

Sessions, R. B., P. Dauber-Osguthorpe & D. Osguthorpe (1989). Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2. J. Mol. Biol. 209, 617-633.

Shapiro, A., J. D. Botha, A. Pastore & A. M. Lesk (1992). A Method for the Multiple Superposition of Structures. Acta. Cryst. A48, 11-14.

Sharp, K. A. & B. Honig (1990). Electrostatic interactions in macromolecules. Annu. Rev. Biophys. Biophys. Chem. 19, 301-32.

Sharp, K. A., A. Nicholls, R. F. Fine & B. Honig (1991). Reconciling the Magnitude of the Microscopic and Macroscopic Hydrophobic Effects. Science 252, 106-109.

Shoichet, B. K. & I. D. Kuntz (1991). Protein Docking and Complementarity. J. Mol. Biol. 221, 327-346.

Siepmann, J. I. (1991). Monte Carlo Calculations for Monolayer Systems. Cambridge University.

Skarzynski, T., P. C. E. Moody & A. J. Wonacott (1987). Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. J. Mol. Biol. 193, 171.

Skarzynski, T. & A. J. Wonacott (1988). Coenzyme-induced Conformational Changes in Glyceraldehyde-3-phosphate Dehydrogenase from Bacillus stearothermophilus. J. Mol. Biol. 203, 1097-1118.

Speedy, R. J., J. D. Madura & W. L. Jorgensen (1987). Network Topology in Simulated Water. J. Phys. Chem. 91, 909-913.

Spurlino, J. C., G. Y. Lu & F. A. Quiocho (1991). The 2.3 Å Resolution Structure of the Maltose-binding or Maltodextrin-binding Protein, a Primary Receptor of Bacterial Active-transport and Chemotaxis. J. Biol. Chem. 266, 5202-5219.

Stallman, R. (1986). GNU Emacs Manual. Sixth Edition, Version 18. Cambridge, MA: Free Software Foundation Inc.

Stone, A. J. (1981). Mol. Phys. 43, 233-248.

Stryer, L. (1988). Biochemistry. 3rd. New York: W H Freeman and Company.

Suh, S. W., T. N. Bhat, M. A. Navia, G. H. Cohen, D. N. Rao, S. Rudikoff & D. R. Davies (1986). The galactan-binding immunoglobulin Fab J539. An X-ray diffraction study at 2.6 Å resolution. Prot. Struct. Func. Genet. 1, 74.

Teeter, M. M. (1991). Water-protein Interactions: Theory and Experiment. Ann. Rev. Biophys. Biophys. Chem. 20, 577-600.

Thanki, N., J. M. Thornton & J. M. Goodfellow (1988). Distribution of water molecules around amino acid residues in proteins. J. Mol. Biol. 202, 637-657.

Thanki, N., Y. Umrania, J. M. Thornton & J. M. Goodfellow (1991). Analysis of protein main-chain solvation as a function of secondary structure. Journal Of Molecular Biology 221, 669-691.

Thomas, D. J. (1989). A false-colour look-up table for images of large dynamic range. J. Appl. Cryst. 22, 498-99.

Tirado-Rives, J. & W. L. Jorgensen (1990). Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water. J. Am. Chem. Soc. 112, 2773-2781.

Tramantano, A., C. H. Chothia & A. M. Lesk (1989). Structural Determinants of the Conformations of Medium- Sized Loops in Proteins. Proteins 6, 382-394.

Valleau, J. P. & A. A. Gardner (1987). Water-like particles at surfaces. I. The uncharged, unpolarized surface. J. Chem. Phys. 86, 4162-4170.

Verlet, L. (1967). Computer "Experiments" on Classical Fluids. I. Thermodynamic Properties of Lennard-Jones Molecules. Phys. Rev. 159, 98-103.

Vyas, N. K., M. N. Vyas & F. A. Quiocho (1988). Sugar and Signal-transducer Binding Sites of the Escherichia coli Galactose Chemoreceptor Protein. Science 242, 1290.

Waldman, A. D. B., K. W. Hart, A. R. Clarke, D. B. Wigley, D. A. Barstow, T. Atkinson, W. N. Chia & J. J. Holbrook (1988). The Use of a Genetically Engineered Tryptophan to Identify the Movement of a Domain of B. Stearothermophilus Lactate Dehydrogenase with the Process which Limits the Steady-state Turnover of the Enzyme. Biochemical Biophysical Research Communications 150, 752-759.

Wallqvist, A. (1990). Polarizable Water at a Hydrophobic Wall. Chem. Phys. Lett. 165, 437-442.

Wallqvist, A. & B. J. Berne (1985). J. Phys. Chem. 145, 26.

Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Methods In Enzymology 115, 90-112.

Weeks, J. D., D. Chandler & H. C. Andersen (1971). Role of repulsive forces in determining the equilibrium structure of simple liquids. J. Chem. Phys. 54, 5237-5247.

White, J., M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. J. Lentz, I. E. Smiley, S. J. Steindel & M. G. Rossman (1976). A Comparison of the Structures of Apo Dogfish M4 Lactate Dehydrogenase and Its Ternary Complexes. J. Mol. Biol 102, 759-79.

Wilks, H. M., K. W. Hart, R. Feeney, C. R. Dune, H. Muirhead, W. N. Chia, D. Barstow, T. Atkinson, A. R. Clarke & J. J. Holbrook (1988). A Specific Highly Active Malate Dehydrogenase by Redesign of Lactate Dehydrogenase Framework. Science 242,

Wintz, P. A. (1969). Transform picture coding. Proc. IEEE 60, 809-820.

Wirenga, R. K., M. E. M. Noble & R. C. Davenport (1992). Comparison of the Refined Crystal Structures of Liganded and Unliganded Chicken, Yeast and Trypanosomal Triosephosphate Isomerase. J. Mol. Biol. 224, 1115-1126.

Wirenga, R. K., M. E. M. Noble, J. P. M. Postma, H. Groendijk, K. H. Kalk, W. G. J. Hol & F. R. Opperdoes (1991a). The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase. Proteins 10, 995-1015.

Wirenga, R. K., M. E. M. Noble, G. Vriend, S. Nauche & W. G. J. Hol (1991b). Refined 1.83 Å structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M ammonium sulphate. J. Mol. Biol. 220, 995-1015.

Zamyatnin, A. A. (1984). Amino acid, peptide, and protein volume in solution. Ann. Rev. Biophys. Bioeng. 13, 145-65.

Zhang, K. Y. J. & P. Main (1990). Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Cryst. A46, 41-46.

Zichi, D. A. & P. J. Rossky (1985). The equilibrium solvent structure for the solvent-separated hydrophobic bond. J. Chem. Phys. 83, 797-808.

Zichi, D. A. & P. J. Rossky (1986). Solvent molecular dynamics in regions of hydrophobic hydration. J. Chem. Phys. 84, 2814-2822.