Alignment methods

Oiengo C A and W R Taylor 1993. A Local Alignment Method for Protein Structure Motifs. ]ourr Molecular Biology 233 488-497. 

AD Baxevams. Pi actical aspects of multiple sequence alignment. Methods Biochem Anal 39 172-188, 1998. 

Passive Micro-Optical Alignment Methods, edited by Robert A. Boudreau and Sharon M. Boudreau... 

Novel Alignment Method of Small Molecules Using the Hopfield Neural Network. 

The fold prediction rate achieved in this analysis is an even greater improvement over the results achieved with pairwise alignment methods (Fischer and Eisenberg, 1997 Gerstein and Levitt, 1997) than reported previously (Wolf et al., 1999). By contrast, several more recent studies that applied PSSM-based methods to protein sets from individual genomes have reported similar prediction rates (Huynen et al., 1998 Paw-... 

Mastronarde, D.N. (1997) Dual-axis tomography an approach with alignment methods that preserve resolution. J. Struct. Biol, 120, 343-352. 

Second, shielding, colhmation and alignment methods were developed to the extent that aU non-sample scattering was removed from the data. This enabled extremely weak sample reflections to be uncovered, which revealed the unexpected structural complexity that had previously been masked by the lower-quality energy-dispersive data. Thirdly, the first GUI interactive software for integrating full two-dimensional images was developed [30, 162]. 

At the beginning of this chapter we will look into the different automated alignment methods as correct alignment is the first and most important prerequisite for a successful pharmacophore identification process. Further, we will elaborate how essential issues of pharmacophore modeling such as conformational search, pharmacophore feature definitions, compounds structure storage and screening are handled by various available software packages. 

Many of the issues and concerns in the generation of pharmacophore models are inherent in different alignment methods. These issues can be used to differentiate or categorize the plethora of available algorithms. 

All alignment methods require some quantitative measure or fitness function, to assess the degree of overlap between the ligands being aligned and to monitor the progression of that optimization. This is most often manifested as a molecular similarity score or alignment index [22]. 

Alignment methods are also known to combine different optimization methods, such as a genetic algorithm and a directed tweak method [36]. 

Alignment method does the program require pre-alignment of molecules On what basis are the molecules aligned together ... 

Application of Structure-based Alignment Methods for 3D QSAR Analyses... 

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