Inference of macromolecular assemblies from crystalline state.
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[1] R. Sternglanz,et al. Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin. , 2007, Structure.
[2] Ponisseril Somasundaran,et al. ENCYCLOPEDIA OF Surface and Colloid Science , 2006 .
[3] M. Rossmann,et al. Evolution of bacteriophage tails: Structure of T4 gene product 10. , 2006, Journal of molecular biology.
[4] A. Perrakis,et al. Selectivity and promiscuity in Eph receptors. , 2006, Structure.
[5] J. Thornton,et al. A method for localizing ligand binding pockets in protein structures , 2005, Proteins.
[6] J. Thornton,et al. Understanding nature's catalytic toolkit. , 2005, Trends in biochemical sciences.
[7] David D L Minh,et al. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. , 2005, Biophysical journal.
[8] Deok-Soo Kim,et al. A protein domain interaction interface database: InterPare , 2005, BMC Bioinformatics.
[9] R. Arni,et al. Inhibition of myotoxic activity of Bothrops asper myotoxin II by the anti-trypanosomal drug suramin. , 2005, Journal of molecular biology.
[10] Ozlem Keskin,et al. PRISM: protein interactions by structural matching , 2005, Nucleic Acids Res..
[11] Sameer Velankar,et al. E-MSD: an integrated data resource for bioinformatics , 2004, Nucleic Acids Res..
[12] K Henrick,et al. Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .
[13] G. Maley,et al. Three-dimensional structure of the R115E mutant of T4-bacteriophage 2'-deoxycytidylate deaminase. , 2004, Biochemistry.
[14] B. Matthews,et al. Alanine‐scanning mutagenesis of the β‐sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on β‐sheet formation , 2004, Protein science : a publication of the Protein Society.
[15] A. Mitraki,et al. Adenovirus fibre shaft sequences fold into the native triple beta-spiral fold when N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif. , 2004, Journal of molecular biology.
[16] Kim Henrick,et al. Common subgraph isomorphism detection by backtracking search , 2004, Softw. Pract. Exp..
[17] H. Wolfson,et al. A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.
[18] Fumio Arisaka,et al. The bacteriophage T4 DNA injection machine. , 2004, Current opinion in structural biology.
[19] S. White,et al. The crystal structure of the UvsW helicase from bacteriophage T4. , 2003, Structure.
[20] J. Janin,et al. Dissecting subunit interfaces in homodimeric proteins , 2003, Proteins.
[21] Janet M. Thornton,et al. Automatic inference of protein quaternary structure from crystals , 2003 .
[22] Mark J van Raaij,et al. The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. , 2003, Journal of molecular biology.
[23] S. Moréra,et al. Crystal structures of the T4 phage beta-glucosyltransferase and the D100A mutant in complex with UDP-glucose: glucose binding and identification of the catalytic base for a direct displacement mechanism. , 2003, Journal of molecular biology.
[24] Gail J. Bartlett,et al. Using a neural network and spatial clustering to predict the location of active sites in enzymes. , 2003, Journal of molecular biology.
[25] M. Rossmann,et al. Structure and location of gene product 8 in the bacteriophage T4 baseplate. , 2003, Journal of molecular biology.
[26] Richard Lavery,et al. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. , 2003, Nucleic acids research.
[27] S. Moréra,et al. A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog. , 2002, Journal of molecular biology.
[28] Xiaojie Xu,et al. Empirical Aqueous Solvation Models Based on Accessible Surface Areas with Implicit Electrostatics , 2002 .
[29] Cheng Yang,et al. Crystal structures of unligated and CN‐ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV , 2002, Proteins.
[30] Marcel L. Verdonk,et al. The consequences of translational and rotational entropy lost by small molecules on binding to proteins , 2002, J. Comput. Aided Mol. Des..
[31] Dmitri I Svergun,et al. Advances in structure analysis using small-angle scattering in solution. , 2002, Current opinion in structural biology.
[32] J. Janin,et al. Dissecting protein–protein recognition sites , 2002, Proteins.
[33] A. Joachimiak,et al. The MotA transcription factor from bacteriophage T4 contains a novel DNA‐binding domain: the ‘double wing’ motif , 2002, Molecular microbiology.
[34] Fumio Arisaka,et al. Structure of the cell-puncturing device of bacteriophage T4 , 2002, Nature.
[35] S. Miller,et al. Crystal structure of a heat and protease-stable part of the bacteriophage T4 short tail fibre. , 2001, Journal of molecular biology.
[36] D. E. Anderson,et al. Unusual molecular architecture of the Yersinia pestis cytotoxin YopM: a leucine-rich repeat protein with the shortest repeating unit. , 2001, Journal of molecular biology.
[37] J. Janin,et al. High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding. , 2001, Journal of molecular biology.
[38] P. Kollman,et al. Solvation Model Based on Weighted Solvent Accessible Surface Area , 2001 .
[39] D. Suck,et al. Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage. , 2001, Journal of molecular biology.
[40] E. Toone,et al. Thermodynamics of metal ion binding. 1. Metal ion binding by wild-type carbonic anhydrase. , 2001, Biochemistry.
[41] C. Dass. Principles and Practice of Biological Mass Spectrometry , 2000 .
[42] J. Thornton,et al. Discriminating between homodimeric and monomeric proteins in the crystalline state , 2000, Proteins.
[43] M. Rossmann,et al. Structure of bacteriophage T4 gene product 11, the interface between the baseplate and short tail fibers. , 2000, Journal of molecular biology.
[44] J. Thornton,et al. An overview of the structures of protein-DNA complexes , 2000, Genome Biology.
[45] J Kuriyan,et al. Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. , 2000, Journal of molecular biology.
[46] T. Mueser,et al. Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold. , 2000, Journal of molecular biology.
[47] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[48] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[49] P B Sigler,et al. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[50] M. Rossmann,et al. The structure of bacteriophage T4 gene product 9: the trigger for tail contraction. , 1999, Structure.
[51] A. Imberty,et al. T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism. , 1999, Journal of molecular biology.
[52] D. Suck,et al. X‐ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain‐swapped dimer architecture , 1999, The EMBO journal.
[53] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[54] Decamers observed in the crystals of bovine pancreatic trypsin inhibitor. , 1999, Acta crystallographica. Section D, Biological crystallography.
[55] J. Thornton,et al. PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.
[56] Robert Preissner,et al. Dictionary of Interfaces in Proteins (DIP). Data Bank of complementary molecular surface patches , 1998, German Conference on Bioinformatics.
[57] George M. Whitesides,et al. Estimating the Entropic Cost of Self-Assembly of Multiparticle Hydrogen-Bonded Aggregates Based on the Cyanuric Acid·Melamine Lattice , 1998 .
[58] N. Agmon,et al. Diffusion approach to the linear Poisson–Boltzmann equation , 1998 .
[59] M. Sternberg,et al. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.
[60] M. B. Pinto,et al. Optimized δ expansion for relativistic nuclear models , 1997, nucl-th/9709049.
[61] F. Guo,et al. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse , 1997, Nature.
[62] R. Nussinov,et al. Hydrogen bonds and salt bridges across protein-protein interfaces. , 1997, Protein engineering.
[63] J. Deisenhofer,et al. Structural Adaptations in the Specialized Bacteriophage T4 Co-Chaperonin Gp31 Expand the Size of the Anfinsen Cage , 1997, Cell.
[64] S. White,et al. The activation domain of the MotA transcription factor from bacteriophage T4 , 1997, The EMBO journal.
[65] P. Brick,et al. Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy. , 1997, Structure.
[66] H. Wolfson,et al. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. , 1996, Critical reviews in biochemistry and molecular biology.
[67] S. Jones,et al. Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[68] C. Pace,et al. Forces contributing to the conformational stability of proteins , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[69] Charles S. Craik,et al. Protein engineering : principles and practice , 1996 .
[70] J. Cavanagh. Protein NMR Spectroscopy: Principles and Practice , 1995 .
[71] Francis Rodier,et al. Protein–protein interaction at crystal contacts , 1995, Proteins.
[72] A. H. Juffer,et al. Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding , 1995, Protein science : a publication of the Protein Society.
[73] Tony J. You,et al. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. , 1995, Biophysical journal.
[74] Enrico O. Purisima,et al. A simple yet accurate boundary element method for continuum dielectric calculations , 1995, J. Comput. Chem..
[75] J M Thornton,et al. Protein-protein interactions: a review of protein dimer structures. , 1995, Progress in biophysics and molecular biology.
[76] W A Hendrickson,et al. Structure of human chorionic gonadotropin at 2.6 A resolution from MAD analysis of the selenomethionyl protein. , 1994, Structure.
[77] J. Thornton,et al. Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.
[78] S. Betz. Disulfide bonds and the stability of globular proteins , 1993, Protein science : a publication of the Protein Society.
[79] H. Zhou,et al. Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. , 1993, Biophysical journal.
[80] D. Yarmush,et al. The application of chemical studies of human chorionic gonadotropin to visualize its three-dimensional structure. , 1993, Endocrine reviews.
[81] A. Fersht,et al. Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. , 1993, Biochemistry.
[82] Stephen C. Harvey,et al. Finite element approach to the electrostatics of macromolecules with arbitrary geometries , 1993, J. Comput. Chem..
[83] D. Eisenberg,et al. Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.
[84] M. Lewis,et al. Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.
[85] E. Jaynes. The Gibbs Paradox , 1992 .
[86] J. Andrew McCammon,et al. Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence , 1991 .
[87] B. Honig,et al. A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .
[88] H. Scheraga,et al. Empirical solvation models can be used to differentiate native from near‐native conformations of bovine pancreatic trypsin inhibitor , 1991, Proteins.
[89] A. Fersht,et al. Strength and co-operativity of contributions of surface salt bridges to protein stability. , 1990, Journal of molecular biology.
[90] C. Chothia,et al. The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.
[91] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[92] Malcolm E. Davis,et al. Electrostatics in biomolecular structure and dynamics , 1990 .
[93] K. Sharp,et al. Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.
[94] M. Akke,et al. Protein stability and electrostatic interactions between solvent exposed charged side chains , 1990, Proteins.
[95] E. Padlan. On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands , 1990, Proteins.
[96] S. Miller. The structure of interfaces between subunits of dimeric and tetrameric proteins. , 1989, Protein engineering.
[97] A V Finkelstein,et al. The price of lost freedom: entropy of bimolecular complex formation. , 1989, Protein engineering.
[98] Jacopo Tomasi,et al. Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation , 1989 .
[99] J. A. McCammon,et al. Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods , 1989 .
[100] John Skilling,et al. Maximum Entropy and Bayesian Methods , 1989 .
[101] C Chothia,et al. Surface, subunit interfaces and interior of oligomeric proteins. , 1988, Journal of molecular biology.
[102] P. Argos. An investigation of protein subunit and domain interfaces. , 1988, Protein engineering.
[103] K. Sharp,et al. Calculating the electrostatic potential of molecules in solution: Method and error assessment , 1988 .
[104] D. I. Svergun,et al. Structure Analysis by Small-Angle X-Ray and Neutron Scattering , 1987 .
[105] H. Scheraga,et al. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[106] M. James,et al. Rat submaxillary gland serine protease, tonin. Structure solution and refinement at 1.8 A resolution. , 1987, Journal of molecular biology.
[107] A. Fersht. The hydrogen bond in molecular recognition , 1987 .
[108] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[109] R. Zauhar,et al. A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.
[110] M. Perutz,et al. The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. , 1984, Journal of molecular biology.
[111] E. Baker,et al. Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.
[112] Samuel H. Yalkowsky,et al. Solubility of nonelectrolytes in polar solvents. V. Estimation of the solubility of aliphatic monofunctional compounds in water using a molecular surface area approach , 1975 .
[113] C. Chothia,et al. Hydrophobic bonding and accessible surface area in proteins , 1974, Nature.
[114] Robert B. Hermann,et al. Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area , 1972 .
[115] W. Jencks,et al. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[116] C. Kittel. Introduction to solid state physics , 1954 .
[117] M. Born. Volumen und Hydratationswärme der Ionen , 1920 .