Table Of Content

Computers & Chemistry Chemistry * Biochemistry * Molecular Biology Editor: James Crabbe List of Contents and Author Index Volume 20, 1996 omputers Chemistry Chemistry * Biochemistry » Molecular Biology editor James Crabbe Professor of Biochemistry, University of Reading, Wolfson Laboratory, AMS Building, Whiteknights, P.O. Box 228, Reading RG6 2AJ, U.K. consulting editor David Edelson 1107 Kenilworth Road, Tallahassee, FL 32312-3854, U.S.A. editorial board Dr P. H. Andersen Professor Michael Gribskov Professor Isaiah Shavitt Novo Nordisk A/S San Diego Supercomputer Center Department of Chemistry CNS Division P.O. Box 85608, San Diego Ohio State University, Columbus Novo Alle, DK-2880 Bagsvaerd CA 92186-9784, U.S.A. OH 43210, U.S.A. DENMARK Professor Peter A. Kollman Dr Jan Andzelm UDneipvaerrtsimteyn t ofo fC alPihfaorrmniaac,e utSiacna l FraCnhceimsicsot ry PDrecpea‘retsmseonrt To.f SChhiedmai stry BIOSYM/Molecular Simulations Inc. CA 94143, U.S.A. Faculty of Sciences, Kyoto University 9685 Seranton Road, San Diego Kyoto 606, JAPAN CA 92121-3752, U.S.A. Dr A. K. Kohopka BioLingua Research Professor Andrzej Sokalski PDrepoafretsmseonrt Ao.f MC.h emBiostnrdy 1M0D1 432 08R7i9d,g elUi.nSe. A.D rive, Gaithersburg, TMeoclhenciuclaalr UMnoidveelrsliitnyg oLf abWorroactloaryw AMUonSaTsRhA LIUnAi versity, Clayton, Vic. 3169 PDreopafretsmseonrt Joafm eChse miAs.t rMy cC& aBmimocohnem istry W5y0b-.3 70W ysWprioacnlaswk,i egPo OL2A7 ND University of California at San Diego DLarb oJr-atMo.i reC la“vinefroirem ation Génétique & La Jolla, CA 92093-0365, U.S.A. Dr W. R. Taylor Structurale” Professor Afonso Nino LNaatbioornaatlo ryI nsftoirt utMea tfhoerm aMteidciacla l BiRoelsoegayr ch IFFr-Ba1Sn3cM4e-0 C2 NRMSar se3i1l leC hCeemdienx J2o0s eph Alguier EUR.noUin.vd earI snifddoera mda Ctaildcaeat rCaadvseat ilCNliaou-.ld aa 5d MaRneaclh a TLhoen doRni dgNewWa7y , 1AMAil,l EHiNllG LAND 13071 Ciudade Real, SPAIN DLors JA. laFmicokse ttN ational Laboratory Professor lwao Ohmine PInrsotifteuts soRrug jeNre nBaods koTvriicn ajstic Mail Stop K710, Los Alamos Chemistry Department, P.O. Box 1016, 41001 Zagreb NM 87545, U.S.A. Faculty of Science, Nagoya University, CROATIA Furo-cho, Chikusa, Nagoya, JAPAN Dr Johann Gasteiger Dr Arthur Olson Professor Charles L. Wilkins Computer-Chemie-Centrum Research Institute of the Scripps Clinic Department of Chemistry Universitaet Erlangen 10666 North Torrey Pines Road University of California, Riverside 91052 Erlangen, GERMANY La Jolla, CA 92037, U.S.A. CA 92521, U.S.A. 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POSTMASTER: Please send address corrections to Computers and Chemistry, c/o Elsevier Science Inc., 660 White Plains Road, Tarrytown, NY 10591-5153. List of Contents NUMBER 1 OPEN PROBLEMS OF COMPUTATIONAL MOLECULAR BIOLOGY (4) Editorial Andrzej K. Konopka v_ Topics in computational biology Section 1: Methodological Issues in Sequence Research Philipp Bucher, 3 A _ flexible motif search technique based on Kevin Karplus, generalized profiles Nicolas Moeri and Kay Hofmann Michael Gribskov 25 Use of receiver operating characteristic (ROC) and Nina L. Robinson analysis to evaluate sequence matching Brief Communication Colin Martindale and 35 Oligonucleotide frequencies in DNA follow a Yule Andrzej K. Konopka distribution Section 2: Molecular Evolution George i. Bell 41 Evolution of simple sequence repeats Claudia Kappen 49 Theoretical approaches to the analysis of homeobox gene evolution Christopher Wills 61 Improving the analysis of phylogenetic data Section 3: Theoretical Biology Christian V. Forst 69 Chaotic interactions of self-replicating RNA Christian Reidys and 85 Bio-molecular shapes and algebraic structures Peter F. Stadler Robert Rosen 95 Biology and the measurement problem Section 4: Genomics—Software and Database Issues James W. Fickett 103 The gene identification problem: an overview for developers Software Note Jerzy Jurka, CENSOR—a program for identification and elimin- Paul Klonowski, ation of repetitive elements from DNA sequences Vadim Dagman and Paul Pelton Juergen Kleffe, Statistical analysis of GeneMark performance by Klaus Hermann cross-validation and Mark Borodovsky Sherri Matis, Ying Xu, Detection of RNA polymerase || promoters and Manesh Shah, polyadenylation sites in human. DNA sequence Xiaojun Guan, J. Ralph Einstein, Richard Mural and Edward Uberbacher Software Note Graziano Pesole, Databases of mRNA _ untranslated regions for Giorgio Grillo and Metazoa Sabino Liuni NUMBER 2 W. G. Bardsley, Optimal design: a computer program to study the R. M. W. Wood best possible spacing of design points for model and E. M. Melikhova discrimination Tetsuo Morikawa Enumeration of Kekulé structures in polyradical polyhexes César Grande Martin, KINAGDC-MW: a multipurpose program for the José Luis Gonzalez treatment of kinetic and equilibrium data Hernandez and M. M. Canedo Alonso R. Cela and M. Lores PREOPT-W: a simulation program for off-line optimization of binary gradient separations in HPLC—I. Fundamentals and overview R. Cela and M. Lores PREOPT-W: a simulation program for off-line optimization of binary gradient separations in HPLC—I|. Data management and miscellaneous aspects of use Roman Wojsz Microcomputer program for the determination of curves characterizing the texture of microporous adsorbents R. S. Stojanovic, Versatile computer-based instrumentation for the H. B. Greenhill, application of three-dimensional voltammetry A. M. Bond and J. E. Anderson Jean-Claude Lartigue, A fast algorithm for computer simulations in INEPT Michel Pétraud, experiments Mouna Harket, Bernard De Jeso and Max Ratier Ludovic Mouron, Geometrical analysis of the voids in structural Gilles Roullet, models of molten salts Jean-Jacques Legendre and Gérard Picard Scott Elliott, Mei Shen, A streamlined family photochemistry module C. Y. J. Kao, R. P. Turco reproduces major nonlinearities in the global and Mark Z. Jacobson tropospheric ozone system H. P. Dettmar, Orange juice classification with a biologically based G. S. Barbour, neural network K. T. Blackwell, T. P. Vogl, D. L. Alkon, F. S. Fry Jr, J. E. Totah and T. L. Chambers Software Note Sachiko Okada X-ray crystallographic computer system and Kenji Okada DS*SYSTEM2 for some organic compounds Application Notes Zhang Xiaodong, WHNMR—a universal NMR application package Hu Hongbin, Huai Nian, Shen Lianfang and Ye Chaohui W. M. Goncalves, An algorithm for the matrix representation of ESR W. M. Pontuschka Hamiltonians and J. C. Sartorelli Andrzej Galat A large-scale processing of kinetic data files with derivation of the inhibitory constant <X;: an application to proline isomerases Book Review James Crabbe From CA to CAS Online Databases in Chemistry by Hedda Schulz and Ursula Georgy NUMBER 3 R. Cela, E. Leira, PREOPT-W: off-line optimization of binary gradient O. Cabaleiro and M. Lores separations in HPLC by simulation—ll!. Phase 2 and the objective functions R. Cela, E. Leira, PREOPT-W: off-line optimization of binary gradient O. Cabaleiro and M. Lores separations in HPLC by simulation—IV. Phase 3 S. D. Dimitrov Parameter estimation in complicated rational and D. I. Kamenski functions Jon A. Christopher, Algorithms for finding the axis of a helix: fast Rosemarie Swanson rotational and parametric least-squares methods and Thomas O. Baldwin Guntram J. R. Haas Fast recording software with automutic mass and Kurt Kalcher calibration for the laser-microprobe-mass-analyzer LAMMA-500 Vv G. V. R. Chandramouli, Fitting of magnetic susceptibility data as a C. Balagopalakrishna, ‘function of temperature of various spin systems—a M. V. Rajasekharan FORTRAN program and P. T. Manoharan Nigel P. Brown, A protein structure comparison methodology Christine A. Orengo and William R. Taylor Software Notes David N. J. White A hardware and software environment for parallel processing with PCs M. P. Garcia Armada A program for calculation and graphic representation of conditional constants—II. Solubility products NUMBER 4 Hanno Essén 389 Calculation of coordinates from molecular geometric and Mats Svensson parameters and the concept of a geometric calculator T. E. Simos and G. Tougelidis 397 A Numerov-type method for computing eigenvalues and resonances of the radial Schrodinger equation Leslaw K. Bieniasz 403 A reaction compiler for electrochemical kinetics Wendell Forst 419 Approximation for sums and densities of state of vibrations coupled with symmetric top K -rotor Roman Wojsz 427 Fractal dimension of microporous carbon on the and Artur P. Terzyk basis of first solution of a Laplace transform using an incomplete gamma function W. J. Melssen, Parallel processing of chemical information in a local E. P. P. A. Derks, area network—l. HYDRA: concept, configuration, M. L. M. Beckers and implementation of parallel applications and L. M. C. Buydens E .P. P. A. Derks, Parallel processing of chemical information in a M. L. M. Beckers, local area network—ll. A parallel cross-validation W. J. Melssen procedure for artificial neural networks and L. M. C. Buydens M. L. M. Beckers, Parallel processing of chemical information in a local E. P. P. A. Derks, area network—lill. Using genetic algorithms for W. J. Melssen, conformational analysis of biomacromolecules and L. M. C. Buydens Frederick H. Hausheer, Ab initio quantum mechanical and X-ray Noel D. Jones, crystallographic studies of gemcitabine and 2'-deoxy P. Seetharamulu, cytosine U. C. Singh, Jack B. Deeter, Larry W. Hertel and Julian S. Kroin Application Notes C. Cruz-Neira, R. Langley VIBE: a virtual biomolecular environment for and P. A. Bash interactive molecular modeling Peter Senn Shaded space-filling stereoscopic representations of molecules as dotted surfaces Software Notes Qyvind Edvardsen A World-Wide Web service for calculating approx- imate AMBER C-C and C-N bond stretching and torsional parameters M. R. Soriano, GAMMEL: a program for the calculation of the J. A. O. Bruno pressure dependence of the elastic constants of ionic and A. Batana crystals Book Review M. G. B. Drew The Art of Molecular Dynamics Simulation by D. C. Rapaport Contents and Author Index for Volume 20, 1996