Searching Algorithm for

TJA Ewing, ID Kuntz. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem 18 1175-1189, 1997. 

Belohlav, Z., P. Zamostny, P. Kluson, and J. Volf, "Application of Random-Search Algorithm for Regression Analysis of Catalytic Hydrogenations", CanJ. Chem. Eng., 75, 735-742 (1997). 

Demirev, P. A. Lin, J. S. Pineda, F. J. Fenselau, C. Bioinformatics and mass spectrometry for microorganism identification Proteome-wide post-translational modifications and database search algorithms for characterization of intact H. Pylori. Anal. Chem. 2001, 73, 4566 573. 

Stein, S. Scott, D.R. Optimization and Testing of Mass Spectral Library Search Algorithms for Compound Identification. J. Am. Soc. Mass Spectrom. 1994, 5, 859-866. 

Qin, Z. S., Gopalakrishnan, S., and Abecasis, G. R. (2006) An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinformatics. 22, 220-225. 

R. J. Dakin. A tree search algorithm for mixed integer programming problems. Computer J., 8 250,1965. 

Since its first introduction in 1982, the DOCK software has been extended in several directions. The matching spheres can be labeled with chemical properties,61 and distance bins are used to speed up the search process.62,63 Recently, the search algorithm for distance-compatible matches was changed28 to the clique-detection algorithm introduced by Crippen and co-workers.55 Furthermore, several scoring functions are now applied in combination with the DOCK algorithm.64-68... 

Search Algorithms for Automated Molecular Docking and Database Screening. 

Search Algorithm for Finding Novel Ligands Capable of Binding Proteins of Known Three-Dimensional Structure. 

A Comparison of Heuristic Search Algorithms for Molecular Docking. 

Thus the search algorithm for the canonical incidence matrix of a hypergraph includes the following steps ... 

R. Everaers and K. Kremer, A fast grid search algorithm for molecular dynamics simulation with short-range interactions, Comput. Phys. Commun., 81 (1994), 19-55. 

The advantage of X-ray powder patterns over other spectra is the roughly common shape of the individual reflections (equal half width and equal shape of the flanks). Therefore, one can use peak search methods that presume a special peak shape. Sanchez (1991) reports a peak search algorithm for Gaussian peaks with an average half width 2D. This method can be easily adapted for Lorentzian peaks (y = A/[l + x — u)/b) ] with FWHM = 2b) or Pearson-VII peaks (y = A/[l + ((x- )/b) f with FWHM = 2b-7( 72-l)). X-ray peaks very often exhibit a peak shape with m between 1.5 and 2. 

Wachter, A. Biegler, L.T. On the Implementation of a Primal-Dual Interior Point Filter Line Search Algorithm for Large-Scale Nonlinear Programming, Research Report IBM T, J. Watson Research Center Yorktown, 2004. 

Wachter, A. and Biegler, L. (2006). On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming, Mathematical Programming 106, pp. 25-57. 

Jang, W-H., Hahn, J. and Hall, K. R. (2005), Genetic/quadratic Search Algorithm for Plant Economic Optimizations Using a Process Simulator, Comput. Chem. Eng., 30, pp. 285-294. 

Duchowicz, P.R., Castro, E.A., Fernandez, F.M. and Perez Gonzalez, M. (2005) A new search algorithm for QSPR/QSAR theories normal hoiling points of some organic molecules. Chan. Phys. Lett., 412, 376-380. 

C. M. Deane, T. L. Blundell. A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins. 2000, 40, 135-144. 

M. C. Lawrence and P. C. Davis. CLIX A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. PROTEINS Structure, Function and Genetics, 12 31-41, 1992. 

D. R. Westhead, D. E. Clark, and C. W. Murray. A comparison of heuristic search algorithms for molecular docking. Journal of Computer-Aided Molecular Design, 11 209-228, 1997. 

Cavique L, Rego C, Themido I. A scatter search algorithm for the maximum clique problem, http //hces.bus.olemiss.edu/reports/hces0101.pdf (Accessed on Feb. 28, 2002). 

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