Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology
Edited by Christopher Rawlings, Dominic Clark, Russ Altman, Lawrence Hunter, Thomas Lengauer, and Shoshana Wodak
July 16 – 19, 1995, Cambridge, England. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
Contents
Sponsors / vii
Organizing and Program Committee / ix
Preface / xi
Christopher Rawlings, Dominic Clark, Russ Altman, Lawrence Hunter, Thomas Lengauer, and Shoshana Wodak
Protein Docking: Combining Symbolic Descriptions of Molecular Surfaces and Grid-Based Scoring Functions / 3
Friedrich Ackermann, Grit Herrmann, Franz Kummert, Stefan Posch, Gerhard Sagerer, and Dietmar Schomburg
Characterizing Oriented Protein Structural Sites Using Biochemical Properties / 12
Steven C. Bagley, Liping Wei, Carol Cheng, and Russ B. Altman
The Value of Prior Knowledge in Discovering Motifs with MEME / 21
Timothy L. Bailey and Charles Elkan
Periodic Sequence Patterns in Human Exons / 30
Pierre Baldi, Søren Brunak, Yves Chauvin, Jacob Engelbrecht, and Anders Krogh
Protein Modeling with Hybrid Hidden Markov Model/Neural Network Architectures / 39
Pierre Baldi and Yves Chauvin
Viewing Genome Data as Objects for Application Development / 48
Ellen R. Bergeman, Mark Graves, and Charles B. Lawrence
APIC : A Generic Interface for Sequencing Projects / 57
Gilles Bisson and Alain Garreau
A Specification for Defining and Annotating Regions of Macromolecular Structures / 66
Steven E. Brenner and Tim J. P. Hubbard
Graph-Theoretic Approach to RNA Modeling Using Comparative Data / 75
Robert B. Cary and Gary D. Stormo
Predicting Free Energy Contribution to the Conformational Stability of Folded Proteins From the Residue Sequence with Radial Basis Function Networks / 81
Rita Casadio, Mario Compiani , Piero Fariselli and Francesco Vivarelli
Recognising Promoter Sequences Using An Artificial Immune System / 89
Denise E. Cooke and John E. Hunt
Predicting Protein Folding Classes without Overly Relying on Homology / 98
Mark W. Craven, Richard J. Mural, Loren J. Hauser, and Edward C. Uberbacher
A Divide and Conquer Approach to Multiple Alignment / 107
Andreas Dress, Georg Füllen,, and Sören Perrey
Multiple Alignment Using Hidden Markov Models / 114
Sean R. Eddy
Symbolic Generation and Clustering of RNA 3-D Motifs / 121
Marielle Foucrault and François Major
Reconstruction of Metabolic Networks Using Incomplete Information / 127
Terry Gaasterland and Evgeni Selkov
Automatic RNA Secondary Structure Determination with Stochastic Context-Free Grammars / 136
Leslie Grate
Parallel Sequence Alignment in Limited Space / 145
J. Alicia Grice, Richard Hughey, and Don Speck
Neural Net Representations of Empirical Protein Potentials / 154
Tal Grossman, Robert Farber, and Alan Lapedes
Classifying Nucleic Acid Sub-Sequences as Introns or Exons Using Genetic Programming / 162
Simon Handley
Constituting a Receptor-Ligand Information Base from Quality-Enriched Data / 170
Klemens Hemm, Karl Aberer, and Manfred Hendlich
3-D Lookup: Fast Protein Structure Database Searches at 90 % Reliability / 179
Liisa Holm and Chris Sander
Evaluating Regularizers for Estimating Distributions of Amino Acids / 188
Kevin Karplus
Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences / 197
Alexander E. Kel, Y. V. Kondrakhin , Ph. A. Kolpakov, O. V. Kel, A. G. Romashenko, E. Wingender, L. Milanesi, and N. A. Kolchanov
Identification of CDNA Sequences by Specific Oligonucleotide Sets--A Computer Tool and Application / 206
N. A. Kolchanov, O. V. Vishnevsky, V. N. Babenko, A. E. Kel, and I. N. Shindyalov
Maximum Entropy Weighting of Aligned Sequences of Proteins or DNA / 215
Anders Krogh and Graeme Mitchison
An Optimized Parsing Algorithm Well Suited to RNA Folding / 222
Fabrice Lefebvre
A Constraint-Based Assignment System for Automating Long Side Chain Assignments in Protein 2D NMR Spectra / 231
Scott Leishman, Peter M. D. Gray, and John E. Fothergill
Relation Between Protein Structure, Sequence Homology and Composition of Amino Acids / 240
Eddy Mayoraz, Inna Dubchak, and Ilya Muchnik
Cooperative Computer System For Genome Sequence Analysis / 249
Claudine Médigue, T. Vermat, G. Bisson, A. Viari, and A. Danchin
MMDB: An ASN.1 Specification for Macromolecular Structure / 259
Hitomi Ohkawa, James Ostell, and Stephen Bryant
Softening Constraints in Constraint-Based Protein Topology Prediction / 268
Simon Parsons
DNA Sequence Assembly and Genetic Algorithms -- New Results and Puzzling Insights / 277
Rebecca Parsons and Mark E. Johnson
A New Approach to Primer Selection in Polymerase Chain Reaction Experiments / 285
William R. Pearson, Gabriel Robins, Dallas E. Wrege, and Tongtong Zhang
Investigations of Escherichia coli Promoter Sequences with Artificial Neural Networks: New Signals Discovered Upstream of the Transcriptional Startpoint / 292
Anders Gorm Pedersen and Jacob Engelbrecht
Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins / 300
Matthias Rarey, Bernd Kramer, and Thomas Lengauer
Subclass Approach for Mutational Spectrum Analysis / 309
Igor B. Rogozin, Galina V. Glasko, and Evgeniy I. Latkin
TOPITS: Threading One-Dimensional Predictions Into Three-Dimensional Structures / 314
Burkhard Rost
A Distance-Based Block Searching Algorithm / 322
Marie-France Sagot, Alain Viari, and Henri Soldano
Using Temporal Reasoning for Genome Map Assembly / 332
Olivier Schmeltzer
Automata--Theoretic Models of Mutation and Alignment / 341
David B. Searls and Kevin P. Murphy
Solvent Accessible Surface Representation in a Database System for Protein Docking / 350
Thomas Seidl and Hans-Peter Kriegel
BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences / 359
Takayoshi Shoudai, Michael Lappe, Satoru Miyano, Ayumi Shinohara, Takeo Okazaki, Setsuo Arikawa, Tomoyuki Uchida, Shinichi Shimozono, Takeshi Shinohara, and Satoru Kuhara
Identification of Human Gene Structure Using Linear Discriminant Functions and Dynamic Programming / 367
Victor A. Solovyev, Asaf A. Salamov, and Charles B. Lawrence
Towards an Intelligent System for the Automatic Assignment of Domains in Globular Proteins / 376
Michael J. E. Sternberg, Hedvig Hegyi, Suhail A. Islam, Jingchu Luo, and Robert B. Russell
Recursive Dynamic Programming for Adaptive Sequence and Structure Alignment / 384
Ralf Thiele, Ralf Zimmer, and Thomas Lengauer
Neweyes: A System for Comparing Biological Sequences Using the Running Karp-Rabin Greedy String-Tiling Algorithm / 393
Michael J. Wise
Identification of Protein Motifs Using Conserved Amino Acid Properties and Partitioning Techniques / 402
Thomas D. Wu and Douglas L. Brutlag
Index / 411