Flexibility in 3D Structure Searching

Piela et al. smooth E by adding in its weighted second derivative, which tends to raise minima (since there the second derivative is positive) and lower maxima. If we think of the original, difficult energy function as E(x, t = 0), then solving the diffusion equation 

In practice, it has been more efficient to abandon the idea of a smooth transformation of the problem in favor of a wider exploration. For example, the idea of dihedral angles can be generalized to many dimensions, and then the return to three dimensions corresponds to making many choices of 0 vs. n in the hyper-dihedral angles, just as one would convert a three-dimensional chain of atoms to a two-dimensional conformation by setting each bond to either cis or trans. Furthermore, the 

The general homotopy approach has inspired a number of different ways to solve difficult problems in computational chemistry. It allows one to exploit various insights into the structure of the problem so as to circumvent seemingly impossible barriers to success. Future developments depend on the next, unpredictable, bright idea. 

Allgowerand K. Georg, Numerical Continuation Methods. An Introduction , Springer Series in Computational Mathematics, Vol. 13, Springer-Verlag, Berlin, 1990. 

ACE = angiotensin converting enzyme BFGS optimization = Broyden-Fletcher-Goldfarb-Shanno optimization CFS search = conformationally flexible structure search CNS central nervous system CSD = Cambridge Structural Database PDB = Brookhaven Protein Data Bank SBDD = structure-based drug design. 

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Comparative Molecular Field Analysis (CoMFA) Conformational Flexibility in 3D Structure Searching Conformational Search Medium-sized Molecules Conformational Search Proteins Genetic and Evolutionary Algorithms Molecular Docking and Structure-based Design Shape Analysis Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases. 

Conformational Flexibility in 3D Structure Searching Machine Learning Techniques in Chemistry Molecular Dynamics Simulations of Nucleic Acids Nucleic Acid Conformation and Flexibility Modeling Using Molecular... 

Experience has shown that retrieval based on 3D geometric cues often returns structures in very different chemical classes as compared with the compound from which the query originated. For additional information see also Conformational Flexibility in 3D Structure Searching and Three-dimensional Structure Searching. 

Computer Graphics and Molecular Modeling Conformational Flexibility in 3D Structure Searching Internet Internet-based Computational Chemistry Tools Molecular Superposition Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules ... 

All G. dzkabak MDL Information Systems, San Leandro, CA, USA Conformational Flexibility in 3D Structure Searching 1 543... 

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