Table of Contents

• Protein Docking: Combining Symbolic Descriptions of Molecular Surfaces and Grid-Based Scoring FunctionsFriedrich Ackermann, Grit Herrmann, Franz Kummert, Stefan Posch, Gerhard Sagerer, Dietmar Schomburg. 3-11
• Characterizing Oriented Protein Structural Sites Using Biochemical PropertiesSteven C. Bagley, Liping Wei, Carol Cheng, Russ B. Altman. 12-20
• The Value of Prior Knowledge in Discovering Motifs with MEMETimothy L. Bailey, Charles Elkan. 21-29
• Periodic Sequence Patterns in Human ExonsPierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, Anders Krogh. 30-38
• Protein Modeling with Hybrid Hidden Markov Model/Neural Network ArchitecturesPierre Baldi, Yves Chauvin. 39-47
• Viewing Genome Data as Objects for Application DevelopmentEllen R. Bergeman, Mark Graves, Charles B. Lawrence. 48-56
• APIC : A Generic Interface for Sequencing ProjectsGilles Bisson, Alain Garreau. 57-65
• A Specification for Defining and Annotating Regions of Macromolecular StructuresSteven E. Brenner, Tim J. P. Hubbard. 66-74
• Graph-Theoretic Approach to RNA Modeling Using Comparative DataRobert B. Cary, Gary D. Stormo. 75-80
• Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function NetworksRita Casadio, Mario Compiani, Piero Fariselli, Francesco Vivarelli. 81-88
• Recognising Promoter Sequences Using An Artificial Immune SystemDenise E. Cooke, John E. Hunt. 89-97
• Predicting Protein Folding Classes without Overly Relying on HomologyMark Craven, Richard J. Mural, Loren J. Hauser, Edward C. Uberbacher. 98-106
• A Divide and Conquer Approach to Multiple AlignmentAndreas W. M. Dress, Georg Füllen, Sören Perrey. 107-113
• Multiple Alignment Using Hidden Markov ModelsSean R. Eddy. 114-120
• Symbolic Generation and Clustering of RNA 3-D MotifsMarielle Foucrault, François Major. 121-126
• Reconstruction of Metabolic Networks Using Incomplete InformationTerry Gaasterland, Evgeni Selkov. 127-135
• Automatic RNA Secondary Structure Determination with Stochastic Context-Free GrammarsLeslie Grate. 136-144
• Parallel Sequence Alignment in Limited SpaceJ. Alicia Grice, Richard Hughey, Don Speck. 145-153
• Neural Net Representations of Empirical Protein PotentialsTal Grossman, Robert M. Farber, Alan S. Lapedes. 154-161
• Classifying Nucleic Acid Sub-Sequences as Introns or Exons Using Genetic ProgrammingSimon Handley. 162-169
• Constituting a Receptor-Ligand Information Base from Quality-Enriched DataKlemens Hemm, Karl Aberer, Manfred Hendlich. 170-178
• 3-D Lookup: Fast Protein Structure Database Searches at 90 ReliabilityLiisa Holm, Chris Sander. 179-187
• Evaluating Regularizers for Estimating Distributions of Amino AcidsKevin Karplus. 188-196
• Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic SequencesAlexander E. Kel, Y. V. Kondrakhin, Ph. A. Kolpakov, O. V. Kel, Aida G. Romashchenko, Edgar Wingender, Luciano Milanesi, Nikolay A. Kolchanov. 197-205
• Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and ApplicationNikolay A. Kolchanov, Oleg V. Vishnevsky, Vladimir N. Babenko, Alexander E. Kel, Ilya N. Shindyalov. 206-214
• Maximum Entropy Weighting of Aligned Sequences of Proteins or DNAAnders Krogh, Graeme J. Mitchison. 215-221
• An Optimized Parsing Algorithm Well Suited to RNA FoldingFabrice Lefebvre. 222-230
• A Constraint-Based Assignment System for Automating Long Side Chain Assignments in Protein 2D NMR SpectraScott Leishman, Peter M. D. Gray, John E. Fothergill. 231-239
• Relation Between Protein Structure, Sequence Homology and Composition of Amino AcidsEddy Mayoraz, Inna Dubchak, Ilya B. Muchnik. 240-248
• Cooperative Computer System For Genome Sequence AnalysisClaudine Médigue, Thierry Vermat, Gilles Bisson, Alain Viari, Antoine Danchin. 249-258
• MMDB: An ASN.1 Specification for Macromolecular StructureHitomi Ohkawa, James Ostell, Stephen H. Bryant. 259-267
• Softening Constraints in Constraint-Based Protein Topology PredictionSimon Parsons. 268-276
• DNA Sequence Assembly and Genetic Algorithms - New Results and Puzzling InsightsRebecca Parsons, Mark E. Johnson. 277-284
• A New Approach to Primer Selection in Polymerase Chain Reaction ExperimentsWilliam R. Pearson, Gabriel Robins, Dallas E. Wrege, Tongtong Zhang. 285-291
• Investigations of Escherichia coli Promoter Sequences with Artificial Neural Networks: New Signals Discovered Upstream of the Transcriptional StartpointAnders Gorm Pedersen, Jacob Engelbrecht. 292-299
• Time-Efficient Docking of Flexible Ligands into Active Sites of ProteinsMatthias Rarey, Bernd Kramer, Thomas Lengauer. 300-308
• Subclass Approach for Mutational Spectrum AnalysisIgor B. Rogozin, Galina V. Glasko, Evgeniy I. Latkin. 309-313
• TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional StructuresBurkhard Rost. 314-321
• A Distance-Based Block Searching AlgorithmMarie-France Sagot, Alain Viari, Henry Soldano. 322-331
• Using Temporal Reasoning for Genome Map AssemblyOlivier Schmeltzer. 332-340
• Automata-Theoretic Models of Mutation and AlignmentDavid B. Searls, Kevin P. Murphy. 341-349
• Solvent Accessible Surface Representation in a Database System for Protein DockingThomas Seidl, Hans-Peter Kriegel. 350-358
• BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid SequencesTakayoshi Shoudai, Michael Lappe, Satoru Miyano, Ayumi Shinohara, Takeo Okazaki, Setsuo Arikawa, Tomoyuki Uchida, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara. 359-358
• Identification of Human Gene Structure Using Linear Discriminant Functions and Dynamic ProgrammingVictor V. Solovyev, Asaf A. Salamov, Charles B. Lawrence. 367-375
• Towards an Intelligent System for the Automatic Assignment of Domains in Globular ProteinsMichael J. E. Sternberg, Hedvig Hegyi, Suhail A. Islam, Jingchu Luo, Robert B. Russell. 376-383
• Recursive Dynamic Programming for Adaptive Sequence and Structure AlignmentRalf Thiele, Ralf Zimmer, Thomas Lengauer. 384-392
• Neweyes: A System for Comparing Biological Sequences Using the Running Karp-Rabin Greedy String-Tiling AlgorithmMichael J. Wise. 393-410
• Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning TechniquesThomas D. Wu, Douglas L. Brutlag. 402-410