Molecular Design and Modeling: Concepts and Applications Part A: Proteins, Peptides, and Enzymes

Content: 
Contributors to volume 202
Pages ix-xii

Preface
Page xiii
John J. Langone

Volumes in series
Pages xv-xxxi

[1] Electrostatic effects in protein folding, stability, and function Original Research Article
Pages 3-19
N.M. Allewell, H. Oberoi

[2] Hydrophobic potentials from statistical analysis of protein structures Original Research Article
Pages 20-31
Charles E. Lawrence, Stephen H. Bryant

[3] Predicting protein secondary structure based on amino acid sequence Original Research Article
Pages 31-44
Ken Nishikawa, Tamotsu Noguchi

[4] Use of homologous sequences to improve protein secondary structure prediction Original Research Article
Pages 45-59
Thomas Niermann, Kasper Kirschner

[5] Conformation of ОІ hairpins in protein structures: Classification and diversity in homologous structures Original Research Article
Pages 59-82
Bancinyane Lynn Sibanda, Janet M. Thornton

[6] Protein engineering in analysis of protein folding pathways and stability Original Research Article
Pages 82-112
Andreas Matouschek, Alan R. Fersht

[7] Mutatational analysis of protein folding mechanisms Original Research Article
Pages 113-126
Patricia A. Jennings, Susanne M. Saalau-Bethell, Bryan E. Finn, Xiaowu Chen, C.Robert Matthews

[8] Clefts and binding sites in protein receptors Original Research Article
Pages 126-156
Richard A. Lewis

[9] Modeling of side chains, loops, and insertions in proteins Original Research Article
Pages 156-204
Neena L. Summers, Martin Karplus

[10] Neural networks for protein structure prediction Original Research Article
Pages 204-224
L.Howard Holley, Martin Karplus

[11] Prediction of О± helices and T cell-presented sequences in proteins with algorithms based on strip-of-helix hydrophobicity index Original Research Article
Pages 225-238
Victor E. Reyes, Robert A. Lew, Shan Lu, Robert E. Humphreys

[12] Comparative modeling of homologous proteins Original Research Article
Pages 239-252
Jonathan Greer

[13] Pattern-based approaches to protein structure prediction Original Research Article
Pages 252-268
Bruce I. Cohen, Scott R. Presnell, Fred E. Cohen

[14] Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data Original Research Article
Pages 268-300
Jacob De Vlieg, Wilfred F. Van Gunsteren

[15] Biosynthetic method for introducing unnatural amino acids site-specifically into proteins Original Research Article
Pages 301-336
Jon Ellman, David Mendel, Spencer Anthony-Cahill, Christopher J. Noren, Peter G. Schultz

[16] Stabilization of functional proteins by introduction of multiple disulfide bonds Original Research Article
Pages 336-356
Masazumi Matsumura, Brian W. Matthews

[17] Complete mutagenesis of protein coding domains Original Research Article
Pages 356-390
Clyde A. Hutchison III, Ronald Swanstrom, Daniel D. Loeb

[18] Systematic mutational analyses of protein-protein interfaces Original Research Article
Pages 390-411
James A. Wells

[19] Aspects of the design of conformationally constrained peptides Original Research Article
Pages 411-436
Paul E. Smith, Fahad Al-Obeidi, B. Montgomery Pettitt

[20] Design of minimum active fragments of biologically active peptides Original Research Article
Pages 436-448
William M. Bryan

[21] Molecular modeling and dynamics of biologically active peptides: Application to neuropeptide Y Original Research Article
Pages 449-470
Alexander D. MacKerell Jr.

[22] Diffusion-controlled enzymatic reactions Original Research Article
Pages 473-497
Malcolm E. Davis, Jeffry D. Madura, Jacqueline Sines, Brock A. Luty, Stuart A. Allison, J. Andrew^McCammon

[23] Theoretical calculations of relative affinities of binding Original Research Article
Pages 497-511
T.P. Straatsma, J.A. McCammon

[24] Quantitative structure-activity relationships and molecular graphics in evaluation of enzyme-ligand interactions Original Research Article
Pages 512-516,IN1-IN2,517-543
Corwin Hansch, Teri E. Klein

[25] Hydrophobic parameter: Measurement and calculation Original Research Article
Pages 544-591
Albert J. Leo

[26] Enzymatic catalysis in organic synthesis Original Research Article
Pages 591-620
C.-H. Wong, G.-J. Shen, R.L. Pederson, Y.-F. Wang, W.J. Hennen

[27] Modification of enzyme catalysis by engineering surface charge Original Research Article
Pages 620-643
Gregorio Alvaro, Alan J. Russell

[28] Mutational remodeling of enzyme specificity Original Research Article
Pages 643-671
Roger Bone, David A. Agard

[29] Modulation of enzyme specificity by site-directed mutagenesis Original Research Article
Pages 671-687
Lizbeth Hedstrom, Laszlo Graf, Caro-Beth Stewart, William J. Rutter, Margaret A. Phillips

[30] Analysis of structure-function relationships by formation of chimeric enzymes produced by gene fusion Original Research Article
Pages 687-706
Melinda E. Wales, James R. Wild

[31] Generation of allosteric enzymes from nonallosteric forms Original Research Article
Pages 706-727
Lawrence C. Kuo

[32] Modeling of structure of human immunodeficiency virus-1 protease with substrate based on crystal structure of rous sarcoma virus protease Original Research Article
Pages 727-741
Irene T. Weber

[33] Modulation of specificity and activity in mammalian cytochrome P-450 Original Research Article
Pages 741-752
Raia L.P. Lindberg, Masahiko Negishi

[34] Previously published articles from methods in enzymology related to molecular design and modeling
Pages 755-760

Author index
Pages 761-798

Subject index
Pages 799-824