Table Of Content

List of Contents and Author Index for Computers and Chemistry Volume 23 Computers 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 DUneipvaerrstimteyn t of ofC alPihfaorrnmiaa,c eutSiacna lF raCnhceimsicsot ry PDrepoafretsmseonrt To.f SChhiedmai stry CA 94143, U.S.A Faculty of Sciences, Kyoto University Kyoto 606, JAPAN Dr A. K. Konopka PDMreoponafarestshms eonrUt n ivAeo.rf s iMCt.yh, e mBisoCtlnardyy t or B1Mi0Do1 L4i32n 0g8uR7ai9 d,g eRleUis.neSea. rAc Dhr ive, Gaithersburg PMToerclohefnceiusclasalor r UMnAoindvederlrslziietnjyg oSLfo akbWaorlrosacktloiar wy AUSTRALIA Professor James A. McCammon Wyb. Wyspianskiego 27 Department of Chemistry & Biochemistry 50-370 Wroclaw, POLAND Dr J-M. Claverie University of California at San Diego Laboratoire ‘Information Génétique & La Jolla, CA 92093-0365, U.S.A Dr W. R. Taylor ISFFt-BRr1ASu3cNM4tC-u0rE2Ca NleRM Sar sei3l1 leC hCeemdienx 2J0o seph Alguier URPE.norUi.no vdfeaerI ssnsifdooderra md aC taAildfacetoa r nCasavdsoaet ilCNlNioai.u- nldaao 5d MaRneaclh a LNLTaahotebni odoroRnanaitl do greNyIw Wnas7yfto ,irt u1tMAeMaA it,l flho erm EHiaNMltleG idcLiacAlaN lD B iRoelsoegayr ch Dr J. Fickett 13071 Ciudade Real, SPAIN SMP7maA0ii9 lt h1S9KC4wlo0ied6nde,ee laUUBnW.edS e .cA2h R2ao3ma0 d PhKairnmga coefu tPircuaslssia CPFFhaurcerouomfl-ietcsysht osr,oyo r f CDShcleiiwpkeaaunrscoaet ,,m eOnhNNtmaa iggonoyyeaa, UJnAivPeArsNi ty CIPPn.rRsOo.tO ifAteuTBts oIsxAoR ru g1j0e1Nr6e ,n Bao4ds1 k0o0Tv1ri icn Zaajgsrteibc Dr Johann Gasteiger Dr Arthur Olson Professor Charles L. Wilkins Computer-Chemie-Centrum Research Institute of the Scripps Clinic Department of Chemistry and Biochemistry Universitaet Erlangen 10666 North Torrey Pines Road University of Arkansas, Fayetteville 91052 Erlangen, GERMANY La Jolla, CA 92037, U.S.A AR 72701, U.S.A Publishing and Advertising Offices Eastpark, Shannon, Co. Clare lreland. Tel 353) 61 709600, Fax: ( + 353) 61 709100/709101. 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Computers & Chemistry (ISSN 0097-8485) is published bimonthly in January, March, May, July, September and November by Elsevier Science Ltd., The Boulevard, Lang ford Lane Kidlington, Oxford OX5 1GB, UK. The US subscription price is $1102.00 per year POSTMASTER: Send address corrections to: Computers & Chemistry, Elsevier Science, Customer Support Department, PO Box 945, New York, NY 10159-0945 Distributed in the USA by Mercury Airfreight International, 365 Blair Road, Avenel, NJ 07001 List of Contents NUMBER 1 T. E. Simos An expert system for the numerical solution of the radial Schrédinger equation J. M. Friedman Interconversion between 3D molecular representations some macromolecular applications of spherical harmonic- Bessel expansions about an arbitrary center V. Alexandrov, |. Filippov, Passing dynamic objects by reference in Fortran 90 L. Adamowicz and application to time-dependent quantum chemistry W. R. Salzman K. Johannsen and D. Britz Matrix stability of the backward differentiation formula in electrochemical digital simulation A. A. Dobrynin A simple formula for the calculation of the wiener index of hexagonal chains M. Karelson and A. Perkson OSPR prediction of densities of organic liquids Shu Tao, Kin Che Lam, Jun Cao Computer simulation of metal complex dissociation and Bengang Li during free metal determination using anodic stripping voltammetry B. V. Alekseev, The research computer method of the multiplicity of steady I. V. Kozhevnikov and states of catalytic reactions N. I. Koltsov . M. Figuera and V. Menendez Determination of vibrational energy distribution in excited molecules from experimental data. New program and test Hau-lai Ho, Wai-kuen Cham, Application of biorthogonal wavelet transform to the Foo-tim Chau and compression of ultraviolet-visible spectra Jian-yong Wu Jingke Zhu, Dezhao Chen and Exploration of artificial neural system for simulation of the Pingdong Wu halogen-exchange fluorination reaction Book Review Nenad Trinajstic Phase equilibria, phase diagrams and phase transform- ations—their thermodynamic basis NUMBER 2 J. D. Mozo, M. Dominguez, Automated impedance measurements in electrochemical E. Roldan and cells J. M. Rodriguez Mellado Thy-Hou Lin, Jia-Jiunn Lin, Common structural folds in several protein pairs searched Wen-Jiun Peng and by an iterative superposition algorithm Jin-Hwang Liu J. Szezygiel Diffusion in a bidispersive grain of a reforming catalyst A. J. Goraczko and The prediction of relative abundance of isotopic clusters J. A. Szymura in mass spectrometry of coordination and organometallic compounds Honggqing Cao, Jingxian Yu, The kinetic evolutionary modeling of complex systems of Lishan Kang, Yuping Chen chemical reactions and Yongyan Chen R. Reams, G. Chatham, Determining protein structure using the distance geometry W. Glunt, D. McDonald and program APA T. Hayden Ramaswamy Ramakrishna and Gene identification in bacterial and organellar genomes Ramachandran Srinivasan using GeneScan F. Stevens and T. P. Beebe Jr. Computer modeling of graphite oxidation: differences between monolayer and multilayer etching NUMBERS 3/4 INFORMATICS AND THE GENOME Maxime Crochemore, 187 Preface: Informatics and the Genome Andrzej K. Konopka, Jean-Loup Risler and Pierre Rouze AREA 1: SEQUENCE ANNOTATION, MAP ASSEMBLY AND OTHER ALGORITHMIC ISSUES OF GENOMICS Anders Gorm Pedersen, The biology of eukaryotic promoter prediction—a review Pierre Baldi, Yves Chauvin and Soren Brunak Yves Quentin, 209 Protein-coding region discovery in organisms under- Catherine Voiblet, represented in databases Francis Martin and Gwennaele Fichant Laurence Vignal, 219 A multi-agent system simulating human splice site Frédérique Lisacek, recognition Joél Quinqueten, Yves d’Aubenton-Carafa and Claude Thermes Michael Q. Zhang Promoter analysis of co-regulated genes in the yeast genome Heather Sasinowska and An algorithm for the assembly of robust physical maps Maciek Sasinowski based on a combination of multi-level hybridization data and fingerprinting data AREA 2: SEQUENCE COMPLEXITY AND OTHER STATISTICAL PROPERTIES Andrei Gabrielian and 263 Sequence complexity and DNA curvature Alexander Bolshoy Maxime Crochemore and 275 Zones of low entropy in genomic sequences Renaud Vérin Wentian Li 283 Statistical properties of open reading frames in complete genome sequences AREA 3: SEQUENCE COMPARISON, DATABASES AND DATABASE SEARCHES J-C. Aude, Y. Diaz-Lazcoz, 303 Applications of the pyramidal clustering method to J-J. Codani and J-L. Risler biological objects J. P. Comet, J. C. Aude, Significance of Z-value statistics of Smith—-Waterman E. Glemet, J. L. Risler, scores for protein alignments A. Hénaut, P. P. Slonimski and J. J. Codani Jérome Gouzy, Whole genome protein domain analysis using a new Florence Corpet and method for domain clustering Daniel Kahn Jaap Heringa Two. strategies for sequence comparison: _ profile- preprocessed and secondary structure-induced multiple J. alignment William R. Taylor and 365 Iterated sequence databank search methods Nigel P. Brown AREA 4: RNA STRUCTURE PREDICTION Ye Ding and 387 A Bayesian statistical algorithm for RNA _ secondary Charles E. Lawrence structure prediction Ivo L. Hofacker and 401 Automatic detection of conserved base pairing patterns in Peter F. Stadler RNA virus genomes NUMBER 5 K. Y. Tam BUFMAKE: a computer program to calculate the compositions of buffers of defined buffer capacity and ionic strength for ultra-violet spectrophotometry Kirk J. Ziegler, Leon Lasdon, Optimization models for determining nitric acid equilibria Jerzy Chlistunoff and in supercritical water Keith P. Johnston Aina W. Ravna, A World Wide Web-service to aid the development of Knut E. Schroder and AMBER parameters using analogy to standard parameters @yvind Edvardsen T. E. Simos Dissipative high phase-lag order Numerov-type methods for the numerical solution of the Schrodinger equation Shaoping Chu, Ecodynamics and dissolved gas chemistry routines for Laurie A. McNair, ocean circulation models Scott Elliott, Chung-Chieng A. Lai, Omar A. Hurricane, Richard P. Turco and Richard C. Dugdale Gilles Caporossi, lvan Gutman Variable neighborhood search for extremal graphs IV: and Pierre Hansen Chemical trees with extremal connectivity index Petr Zamostny and A software for regression analysis of kinetic data Zdenek Belohlav Robert A. Marriott. Automated statistical analysis of high temperature and Andrew W. Hakin, pressure vibrating tube densimeter data Jin Lian Liu and Mare R. Roussel Maria Carolina Monard, Calculation of the pressure dependence of anion Alicia Batana and polarizabilities in crystals Jorge A. O. Bruno P. C. Chen, S. C. Tzeng and Molecular structures of dinitroanilines and trinitroanilines F. M. Chang NUMBER 6 T. E. Simos and P. S. Williams On finite difference methods for the solution of the Schrddinger equation B. Zhou, J.-Y. Li, J.-H. Yu, Systematic enumeration of two-dimensional layered Y.-H. Xu, W.-G. Xu, N. Shi, aluminophosphates with [AlsP Ove)" stoichiometry S.-L. Qiu and R.-R. Xu Nicolaas (Klaas) M. Faber Modification of Malinowski's F-test for pseudo rank estimation revisited Andrey A. Dobrynin and The average Wiener index of hexagonal chains Ivan Gutman Andy Cheok-man Chan, Application of image analysis techniques to two- Samuel Chun-lap Lo, dimensional crossed immunoelectrophoresis study Foo-tim Chau and Alexander Kai-man Leung Jan Mikulas Lisy, Peter Simon, Least squares estimation of parameters in implicit models Sona Bafrncova and Elena Graczova Stéphane Noury, Computational tools for the electron localization function Xénophon Krokidis, topological analysis Franck Fuster and Bernard Silvi Book Reviews Gail Hutchinson Introduction to Bioinformatics Gail Hutchinson Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding M. James and C. Crabbe Molecular Simulation of Fluids; Theory, Algorithms and Object-orientation AUTHOR INDEX Adamowicz L., 25 Goraczko A. J., 135 Qiu S.-L., 555 Alekseev B. V., 69 Gouzy J., 333 Quentin Y., 209 Alexandrov V., 25 Graczova E., 587 Quinqueton J d‘Aubenton-Carafa Y., 219 Gutman |., 469, 571 Aude J. C., 317 Ramakrishna R., 165 Aude J.-C., 303 Hakin A. W., 487 Ravna A. W., 435 Hansen P., 469 Reams R., 153 Bafrncova S., 587 Hayden T., 153 Risler J. L., 317 Baldi P., 191 Hénaut A., 317 Risler J.-L., 187, 303 Batana A., 493 Heringa J., 341 Roldan E., 101 Beebe Jr. T. P., 175 Ho H.-l., 85 Roussel M. R., 487 Belohlav Z., 479 Hofacker |. L., 401 Rouzé P., 187 Bolshoy A., 263 HurricaneO . A., 447 Britz D., 33 Hutchinson G., 605, 607 Salzman W. R Brown N. P., 365 Sasinowska H Brunak S., 191 James M., 609 Sasinowski M Bruno J. A. O., 493 Johannsen K., 33 Schroder K. E Johnston K. P., 421 Shi N., 555 Cao H., 143 Silvi B., 597 Cao J., 61 Kahn D., 333 Simon P., 587 Caporossi G., 469 Kang L., 143 Simos T. E Cham W.-k., 85 Karelson M., 49 Slonimski Chan A. C.-m., 577 Koltsov N. |., 69 Srinivasan Chang F. M., 503 Konopka A. K., 187 Stadler P Chatham G., 153 Kozhevnikov |. V., 69 Stevens F., 17 Chau F.-t., 85, 577 Krokidis X., 597 Szezygiet J., Chauvin Y., 191 Szymura J Chen D., 97 Lai C.-C. A., 447 Chen P. C., 503 Lam K. C., 61 CChhleins tuYn.o, ff1 43,J. , 144231 Lasdon L., 421 TTaaom S.K,. 6Y1 CCohdua nSi. , J4. 47J ., 317 LLeauwnrge ncAe. KC..- m.,E. , 358777 TTahyelromr esW . C.,R ., 21396 5 Codani J.-J., 303 Trinajsti¢ N., 101 Comet J. P., 317 TurcoR . P., 447 Corpet F., 333 Tzeng S. C., 503 Crabbe C., 609 Crochemore M., 187, 275 Vignal L Lisacek F Vérin R Diaz-Lazcoz Y., 303 Lisy J. M., § Voiblet C liad. Ding Y., 387 Liu J Dobrynin A. A., 43, 571 to S.C Dominguez M., 101 Dugdale R. C., 447 Marriott R. A., 487 Edvardsen @., 435 Martin F., 209 Elliott S., 447 McDonald D., 153 McNair L. A., 447 Faber N. (Klaas) M., 565 Mellado J. M. R., 101 Fichant G., 209 Menendez V., 75 Figuera J. M., 75 Monard M. C., 493 Filippov I., 25 Mozo J. D., 101 Friedman J. M., 9 Fuster F., 597 Noury S., 597 Zamostny P., 479 Zhang M. Q., 233 Gabrielian A., 263 Pedersen A. G., 191 Zhou B., 555 Glémet E., 317 Peng W.-J., 109 Zhu J., 97 Glunt W., 153 Perkson A., 49 Ziegler K. J., 421