Are proteins well-packed?

[1]  D. Raleigh,et al.  A comparative study of peptide models of the alpha-domain of alpha-lactalbumin, lysozyme, and alpha-lactalbumin/lysozyme chimeras allows the elucidation of critical factors that contribute to the ability to form stable partially folded states. , 2001, Biochemistry.

[2]  B. Honig Protein folding: from the levinthal paradox to structure prediction. , 1999, Journal of molecular biology.

[3]  C. Chothia,et al.  The Packing Density in Proteins: Standard Radii and Volumes , 1999 .

[4]  M. Zalis,et al.  Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.

[5]  Herbert Edelsbrunner,et al.  On the Definition and the Construction of Pockets in Macromolecules , 1998, Discret. Appl. Math..

[6]  S Subramaniam,et al.  Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape , 1998, Proteins.

[7]  H Edelsbrunner,et al.  Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins , 1998, Proteins.

[8]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

[9]  M. McGee,et al.  Hydration structure of antithrombin conformers and water transfer during reactive loop insertion. , 1998, Biophysical journal.

[10]  M. McGee,et al.  structure–function relationships of the , 2022 .

[11]  J. O´Rourke,et al.  Computational Geometry in C: Arrangements , 1998 .

[12]  J Liang,et al.  Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[13]  F. Stillinger,et al.  Statistical geometry of particle packings. I. Algorithm for exact determination of connectivity, volume, and surface areas of void space in monodisperse and polydisperse sphere packings , 1997 .

[14]  S Subramaniam,et al.  Computation of molecular electrostatics with boundary element methods. , 1997, Biophysical journal.

[15]  Herbert Edelsbrunner,et al.  Triangulating the Surface of a Molecule , 1996, Discret. Appl. Math..

[16]  M Gerstein,et al.  Packing at the protein-water interface. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[17]  A. Fersht,et al.  Active barnase variants with completely random hydrophobic cores. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[18]  C. Frömmel,et al.  The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. , 1996, Journal of molecular biology.

[19]  van der Marck SC Network Approach to Void Percolation in a Pack of Unequal Spheres. , 1996, Physical review letters.

[20]  J. Sturtevant,et al.  Thermodynamics of the thermal unfolding of eglin c in the presence and absence of guanidinium chloride. , 1995, Biophysical chemistry.

[21]  M. Levitt,et al.  The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. , 1995, Journal of molecular biology.

[22]  Michael A. Facello,et al.  Implementation of a randomized algorithm for Delaunay and regular triangulations in three dimensions , 1995, Comput. Aided Geom. Des..

[23]  Herbert Edelsbrunner,et al.  Measuring proteins and voids in proteins , 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

[24]  P. Privalov,et al.  Energetics of protein structure. , 1995, Advances in protein chemistry.

[25]  Joseph O'Rourke,et al.  Computational Geometry in C. , 1995 .

[26]  P. Argos,et al.  Cavities and packing at protein interfaces , 1994, Protein science : a publication of the Protein Society.

[27]  A M Gronenborn,et al.  Thermodynamics of unfolding of the all beta-sheet protein interleukin-1 beta. , 1994, Biochemistry.

[28]  K A Dill,et al.  Side‐chain entropy and packing in proteins , 1994, Protein science : a publication of the Protein Society.

[29]  M Gerstein,et al.  Volume changes on protein folding. , 1994, Structure.

[30]  Michel Petitjean,et al.  On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects , 1994, J. Comput. Chem..

[31]  P Argos,et al.  Intramolecular cavities in globular proteins. , 1994, Protein engineering.

[32]  R. Meester,et al.  Nonuniversality and continuity of the critical covered volume fraction in continuum percolation , 1994 .

[33]  P. Privalov,et al.  Thermodynamics of barnase unfolding , 1994, Protein science : a publication of the Protein Society.

[34]  C. Pace,et al.  Energetics of ribonuclease T1 structure. , 1994, Biochemistry.

[35]  G J Kleywegt,et al.  Detection, delineation, measurement and display of cavities in macromolecular structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[36]  L Serrano,et al.  Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. , 1994, Biochemistry.

[37]  P. Privalov,et al.  Thermodynamics of ubiquitin unfolding , 1994, Proteins.

[38]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[39]  A. Gronenborn,et al.  Thermodynamics of Unfolding of the All ,&Sheet Protein Interleukin- 1 @ , 1994 .

[40]  Clare Woodward,et al.  Thermodynamics of bpti folding , 1993, Protein science : a publication of the Protein Society.

[41]  F M Richards,et al.  An analysis of packing in the protein folding problem , 1993, Quarterly Reviews of Biophysics.

[42]  I. Orgzall,et al.  Universality and cluster structures in continuum models of percolation with two different radius distributions , 1993 .

[43]  Herbert Edelsbrunner,et al.  The union of balls and its dual shape , 1993, SCG '93.

[44]  Ernst P. Mücke,et al.  Three-dimensional alpha shapes , 1992 .

[45]  J. Delaney Finding and filling protein cavities using cellular logic operations. , 1992, Journal of molecular graphics.

[46]  Herbert Edelsbrunner,et al.  Incremental topological flipping works for regular triangulations , 1992, SCG '92.

[47]  P. Alexander,et al.  Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: why small proteins tend to have high denaturation temperatures. , 1992, Biochemistry.

[48]  H. Hinz,et al.  Thermodynamics of unfolding of the alpha-amylase inhibitor tendamistat. Correlations between accessible surface area and heat capacity. , 1992, Journal of molecular biology.

[49]  Akbar Nayeem,et al.  MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives , 1992 .

[50]  K. P. Murphy,et al.  Solid model compounds and the thermodynamics of protein unfolding. , 1991, Journal of molecular biology.

[51]  A. Fersht,et al.  Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. , 1991, Biochemistry.

[52]  Barry Joe,et al.  Construction of three-dimensional Delaunay triangulations using local transformations , 1991, Comput. Aided Geom. Des..

[53]  Chris M. W. Ho,et al.  Cavity search: An algorithm for the isolation and display of cavity-like binding regions , 1990, J. Comput. Aided Mol. Des..

[54]  Estanislao Silla,et al.  GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set , 1990 .

[55]  W E Stites,et al.  Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. , 1990, Biochemistry.

[56]  Harris,et al.  Series study of percolation moments in general dimension. , 1990, Physical review. B, Condensed matter.

[57]  G. Vriend,et al.  A very fast program for visualizing protein surfaces, channels and cavities. , 1989, Journal of molecular graphics.

[58]  W. Lim,et al.  Alternative packing arrangements in the hydrophobic core of λrepresser , 1989, Nature.

[59]  J. Sturtevant,et al.  A scanning calorimetric study of the thermal denaturation of the lysozyme of phage T4 and the Arg 96----His mutant form thereof. , 1989, Biochemistry.

[60]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[61]  K. D. Gibson,et al.  Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii , 1987 .

[62]  Herbert Edelsbrunner,et al.  Algorithms in Combinatorial Geometry , 1987, EATCS Monographs in Theoretical Computer Science.

[63]  B Honig,et al.  Internal cavities and buried waters in globular proteins. , 1986, Biochemistry.

[64]  S. Redner,et al.  Introduction To Percolation Theory , 2018 .

[65]  Michael Ian Shamos,et al.  Computational geometry: an introduction , 1985 .

[66]  T. Richmond,et al.  Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. , 1984, Journal of molecular biology.

[67]  C. Chothia Principles that determine the structure of proteins. , 1984, Annual review of biochemistry.

[68]  M. L. Connolly Analytical molecular surface calculation , 1983 .

[69]  Gérard Viennot,et al.  Algebraic Languages and Polyominoes Enumeration , 1983, Theor. Comput. Sci..

[70]  E. Gratton,et al.  Adiabatic compressibility of globular proteins. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J L Finney,et al.  Calculation of protein volumes: an alternative to the Voronoi procedure. , 1982, Journal of molecular biology.

[72]  P. Mateo,et al.  Pepsinogen denaturation is not a two‐state transition , 1981, FEBS letters.

[73]  D. Hugh Redelmeier,et al.  Counting polyominoes: Yet another attack , 1981, Discret. Math..

[74]  Robin Milner,et al.  On Observing Nondeterminism and Concurrency , 1980, ICALP.

[75]  P. Privalov,et al.  Papain denaturation is not a two‐state transition , 1978, FEBS letters.

[76]  J L Finney,et al.  Volume occupation, environment, and accessibility in proteins. Environment and molecular area of RNase-S. , 1978, Journal of molecular biology.

[77]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[78]  C. Lawson Software for C1 Surface Interpolation , 1977 .

[79]  J L Finney,et al.  Volume occupation, environment and accessibility in proteins. The problem of the protein surface. , 1975, Journal of molecular biology.

[80]  C. Chothia Structural invariants in protein folding , 1975, Nature.

[81]  P. Privalov,et al.  A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. , 1974, Journal of molecular biology.

[82]  F. Richards The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.

[83]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[84]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[85]  J. L. Finney,et al.  Random packings and the structure of simple liquids. I. The geometry of random close packing , 1970, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[86]  S. Lowen The Biophysical Journal , 1960, Nature.