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Conformation search

Figure 4.49 reprinted with permission from Pranata J and W L Jorgensen. Computational Studies on FK506 Conformational Search and Molecular Dynamics Simulations in Water. The Journal of the American Chemical Society 113 9483-9493. 1991 American Chemical Society. [Pg.19]

The input to a minimisation program consists of a set of initial coordinates for the system. The initial coordinates may come from a variety of sources. They may be obtained from an experimental technique, such as X-ray crystallography or NMR. In other cases a theoretical method is employed, such as a conformational search algorithm. A combination of experimenfal and theoretical approaches may also be used. For example, to study the behaviour of a protein in water one may take an X-ray structure of the protein and immerse it in a solvent bath, where the coordinates of the solvent molecules have been obtained from a Monte Carlo or molecular dynamics simulation. [Pg.275]

Tree representation of the conformation search problem for hexane. Unlike the tree in Figure 9.4 the path gth from the root node to any of the terminal nodes is constant. [Pg.478]

Flow chart steps Jbllowed by a random conformational search. [Pg.482]

A comparison of fine different conformational searching algorithms. (Data from [Saunders et at 1990].)... [Pg.492]

Judson R S, W P Jaeger, A M Treasurywala and M L Peterson 1993. Conformational Searching Methods for Small Molecules. 2. Genetic Algorithm Approach. Journal of Computational Chemistry 14 1407-1414. [Pg.523]

Method and a Genetic Algorithm for Conformational Searching. Journal of Computational... [Pg.524]

All of the conformational search methods that were described in Sections 9.2-9.7 have bee used at some stage to explore the conformational space of small pephdes. Here we wi describe some of the methods designed specifically for tackling the problem for peptide and proteins. [Pg.533]

The amount of computation necessary to try many conformers can be greatly reduced if a portion of the structure is known. One way to determine a portion of the structure experimentally is to obtain some of the internuclear distances from two-dimensional NMR experiments, as predicted by the nuclear Over-hauser effect (NOE). Once a set of distances are determined, they can be used as constraints within a conformation search. This has been particularly effective for predicting protein structure since it is very difficult to obtain crystallographic structures of proteins. It is also possible to define distance constraints based on the average bond lengths and angles, if we assume these are fairly rigid while all conformations are accessible. [Pg.185]


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See also in sourсe #XX -- [ Pg.127 , Pg.181 ]

See also in sourсe #XX -- [ Pg.179 , Pg.180 , Pg.181 , Pg.182 , Pg.183 , Pg.184 , Pg.185 , Pg.186 , Pg.187 , Pg.188 , Pg.189 , Pg.190 , Pg.191 ]




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A general method for the searching of conformational space

Active Conformer Searches with the Dynamic Method

Boltzmann distribution, from conformational search

ConFirm conformational searching

Conformation search Molecular geometry

Conformation search Monte Carlo

Conformation search distance-geometry

Conformation search fragment approach

Conformation search genetic algorithm

Conformation search homology

Conformation search ring systems

Conformation search rule-based

Conformation search simulated annealing

Conformational search

Conformational search

Conformational search Molecular dynamics

Conformational search Stochastic

Conformational search linear chains

Conformational search medium-sized molecules

Conformational search method

Conformational search proteins

Conformational search space

Conformational search space, molecular

Conformational search space, molecular contacts

Conformational search techniques

Conformational searching

Conformational searching

Conformational searching Monte-Carlo

Conformational searching complications

Conformational searching evaluation procedure

Conformational searching genetic algorithms

Conformational searching molecular dynamics

Conformational searching systematic

Conformational searching/quenched

Conformational space searching

Conformational-searching procedure

Conformationally flexible searching

Conformer Search

Conformer Search

Dihedral angles conformational search

Exhaustive Conformational Searching Methods

For conformational searching

Fragment-based conformational search

Genetic algorithms conformational search problems

Geometry optimization Conformation search, Molecular

Low-mode conformational search

Molecular conformation conformational search

Molecular contacts, conformational search

Molecular modelling systematic conformational search

Monte Carlo conformational search

Monte Carlo conformational search algorithms

Monte Carlo conformational searche

Random methods conformational searching

Random search through conformational

Random search through conformational space

Ring systems conformational searching

Robust optimizers conformational search

Searching of conformational space

Selectivity systematic conformational search

Side chain conformations search

Stochastic conformational searching

Structure searching conformational flexibility

Systematic and Random Search Methods for Finding Conformers of Molecules

Systematic conformational search representation

Systematic search conformational

Three-dimensional structure searching conformational flexibility

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