Molecular Scene Analysis and Its Role in Protein Structure Determination

The paper presents an introduction to scene analysis, an area of machine vision concerned with the set of processes associated with the reconstruction, classification and interpretation of complex images. Approaches designed to extend scene analysis to the molecular domain and, in particular, to the analysis and interpretation of protein electron density maps are described. Examples are given of applications to protein maps at medium and low resolution.

[1]  Temple F. Smith,et al.  Global optimum protein threading with gapped alignment and empirical pair score functions. , 1996, Journal of molecular biology.

[2]  Z. Jia,et al.  Structural basis for the binding of a globular antifreeze protein to ice , 1996, Nature.

[3]  C. J. Hilditch,et al.  Linear Skeletons From Square Cupboards , 1969 .

[4]  Richard H. Lathrop,et al.  From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination , 1996, ISMB.

[5]  Susan L. Epstein For the Right Reasons: The FORR Architecture for Learning in a Skill Domain , 1994, Cogn. Sci..

[6]  S M Swanson,et al.  Core tracing: depicting connections between features in electron density. , 1994, Acta crystallographica. Section D, Biological crystallography.

[7]  Dauid F. Percy Cluster Analysis (3rd Edition) , 1994 .

[8]  E. Shortliffe Computer-based medical consultations: mycin (elsevier north holland , 1976 .

[9]  G. Sheldrick SHELX Applications to Macromolecules , 1998 .

[10]  D. Marr,et al.  Representation and recognition of the spatial organization of three-dimensional shapes , 1978, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[11]  Ilyas Absar,et al.  XVI. Representations of the Electron Density and its Topographical Features , 1977 .

[12]  Janice I. Glasgow,et al.  Conformational analysis from crystallographic data using conceptual clustering , 1996 .

[13]  Janice I. Glasgow,et al.  Knowledge representation tools for molecular scene analysis , 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

[14]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[15]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[16]  Edward H. Shortliffe,et al.  Computer-based medical consultations, MYCIN , 1976 .

[17]  J Greer Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins. , 1974, Journal of molecular biology.

[18]  M. Kjeldgaard,et al.  O: A Macromolecule Modeling Environment , 1990 .

[19]  H. Hauptman,et al.  On the application of the minimal principle to solve unknown structures. , 1993, Science.

[20]  Janice I. Glasgow,et al.  Spatial Analogy and Subsumption , 1992, ML.

[21]  Kevin Cowtan,et al.  Introduction to Density Modification , 1998 .

[22]  C. Weeks,et al.  Shake-and-Bake : Applications and Advances , 1998 .

[23]  Janice I. Glasgow,et al.  Analysis of Three-Dimensional Protein Images , 1997, J. Artif. Intell. Res..

[24]  M. James,et al.  Structure and refinement of penicillopepsin at 1.8 A resolution. , 1983, Journal of molecular biology.

[25]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[26]  R. Bader Atoms in molecules : a quantum theory , 1990 .

[27]  Jones Ta,et al.  Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. , 1985, Methods in enzymology.

[28]  S Fortier,et al.  Molecular scene analysis: application of a topological approach to the automated interpretation of protein electron-density maps. , 1994, Acta crystallographica. Section D, Biological crystallography.

[29]  Marvin Minsky,et al.  A framework for representing knowledge , 1974 .

[30]  Bernhard Nebel,et al.  Reasoning and Revision in Hybrid Representation Systems , 1990, Lecture Notes in Computer Science.