ARP/wARP's model-building algorithms. I. The main chain.

Algorithms underlying the automatic model-building functionality of the ARP/wARP software suite are presented. Finding the most likely set of Calpha atoms from a given set of atoms is formulated as a constrained integer programming problem. The objective function is a density-weighted score for the match between observed and expected chain conformation. Graph-search algorithms are presented that find solutions to this problem in an efficient manner.

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

[2]  W G Hol,et al.  A database method for automated map interpretation in protein crystallography , 1999, Proteins.

[3]  M. H. J. Koch.  On the application of phase relationships to complex structures. VI. Automatic interpretation of electron-density maps for organic structures , 1974 .

[4]  T A Jones,et al.  Electron-density map interpretation. , 1997, Methods in enzymology.

[5]  M. R. Rao,et al.  Combinatorial Optimization , 1992, NATO ASI Series.

[6]  Richard O. Duda,et al.  Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.

[7]  D. McRee,et al.  A visual protein crystallographic software system for X11/Xview , 1992 .

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

[9]  Keinosuke Fukunaga,et al.  Introduction to statistical pattern recognition (2nd ed.) , 1990 .

[10]  G. Bricogne.  [23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples. , 1997, Methods in enzymology.

[11]  Peter E. Hart,et al.  Pattern classification and scene analysis , 1974, A Wiley-Interscience publication.

[12]  B C Finzel.  LORE: exploiting database of known structures. , 1997, Methods in enzymology.

[13]  G J Kleywegt,et al.  Validation of protein models from Calpha coordinates alone. , 1997, Journal of molecular biology.

[14]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[15]  A. Brunger.  Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[16]  V S Lamzin,et al.  Automated refinement for protein crystallography. , 1997, Methods in enzymology.

[17]  G Bricogne,et al.  Ab initio macromolecular phasing: blueprint for an expert system based on structure factor statistics with built-in stereochemistry. , 1997, Methods in enzymology.

[18]  G J Kleywegt,et al.  Model building and refinement practice. , 1997, Methods in enzymology.

[19]  Robert Sedgewick,et al.  Algorithms in C , 1990 .

[20]  W G Hol,et al.  A rapid method for positioning small flexible molecules, nucleic acids, and large protein fragments in experimental electron density maps , 1999, Proteins.

[21]  S Fortier,et al.  Critical-point analysis in protein electron-density map interpretation. , 1997, Methods in enzymology.

[22]  Wayne A. Hendrickson,et al.  A restrained-parameter thermal-factor refinement procedure , 1980 .