G. M. Crippen and T.F. Havel. Distance Geometry and Molecular Conformation. Wiley, New York, 1988. Home/Search Document Not in Database Summary Related Articles Check |
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Solving the Multiple-Instance Problem with.. - Dietterich, Lathrop, .. (1997) (77 citations) (Correct)
.... Other methods that employ some form of shape representation include Koehler, Rowberg Schaefer Hopfinger (1988) Good, So, Richards (1993) and Vedani, Zginden Snyder (1993) A method that confronts the multiple instance problem directly is the elegant distance geometry approach of Crippen (Crippen Havel, 1988). Unfortunately, combinatorial explosions in the search space of their approach limit the complexity of their binding site hypotheses to constraints on the positions of four or five key atoms. The approach that we describe can learn detailed constraints on the position of the entire molecular ....
Crippen, G. M., & Havel, T. F. (1988). Distance geometry and molecular conformation. New York: John Wiley & Sons.
An infeasible point method for minimizing the Lennard-Jones.. - Gockenbach (1993) (3 citations) (Correct)
....as the problem is transformed back to the original. By combining this idea of reformulating the energy function with a version of simulated annealing and local minimization, the global minimum has been found in a large proportion of attempts for problems with m 27 (see [4] Crippen and Havel ([5]) reformulate the problem by allowing the atoms to move in a higher dimensional Euclidean space. A constraint which enforces the condition that the atoms are actually in 3 space is then added, and the constrained problem is then solved by an augmented Lagrangian algorithm. Although this approach ....
....the condition that the atoms are actually in 3 space is then added, and the constrained problem is then solved by an augmented Lagrangian algorithm. Although this approach does not always find the global solution, it is reported that it tends to find low energy configurations consistently (see [5] and the references therein) 4 3 An Infeasible Point Approach 3.1 Motivation The incredible multiplicity of minima of the Lennard Jones potential is due to the fact that each atom interacts with every other atom. The pair potential itself is relatively simple, having a unique minimum (see ....
G. M. Crippen and T. F. Havel. Distance Geometry and Molecular Conformation, John Wiley & Sons, New York, 1988.
Mathematical Modeling of Protein Structure Using Distance.. - Yoon, Gad, Wu (2000) (Correct)
....by the given distances may not be unique and it may not even exist if the distances are not consistent. In any case, the solution to a distance geometry problem will be able to provide useful information about what the protein structure could be or where the inconsistency may occur in the data [5, 2, 10]. 1.2 Potential Energy Minimization A more general approach to protein structure determination is potential energy minimization, which assumes that the protein structure corresponds to the global minimum of the system s potential energy. Therefore, the structure may be found by minimizing a ....
....we discuss the distance geometry problem. We discuss problem formulations and complexity issues. Three classes of problems are described, including the problems with all exact distances, with sparse sets of distances, and with bounds on the distances. 2. 1 History According to Crippen and Havel [5], the general form of the distance geometry problem was given by Cayley in 1841. The problem was not systematically studied until 1928, when Menger showed how convexity and many other basic geometric properties could be defined and studied in terms of distances between pairs of points. In 1935, ....
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G. M. Crippen and T. F. Havel , Distance Geometry and Molecular Conformation, John Wiley & Sons, 1988.
Protein Folding in Contact Map Space - Domany (Correct)
....backbone. Clearly, the mapping from conformations to contact maps is many to one: many conformations yield the same map. Nevertheless, given all the interresidue contacts or even a subset of them, it is possible to reconstruct quite well a protein s structure, by means of either distance geometry [9], Molecular Dynamics [10] or Monte Carlo [8] In contrast to detailed atomistic representations, in which the Cartesian coordinates of every ion are specified, the map representation of a protein s structure is independent of the coordinate frame. This property made contact maps attractive for ....
G. Crippen and T. F. Havel, Distance geometry and molecular conformation, (Wiley, New York, 1988).
Determining Molecular Conformation from Distance or Density Data - Wang (2000) (3 citations) (Correct)
....results also suggest that experiments should be designed to obtain negative data close to the boundary of detection, thus maximizing information on the structure. For example, if a small set of constraints is known, we can use the triangle inequality to establish upper bounds on other distances[8]. Further experiments can be directed towards measurements with small upper bounds. It should be noted that in certain circumstances, strategically chosen negative constraints may be especially useful; the results here suggest that randomly selected negative constraints are unlikely to be as ....
....may have rings that do not close, or atoms that clash with one another. Therefore, it is necessary to perform a conformational search to nd a structure without any of these violations. The constraints to be satis ed in the search stage, the non local set, are embodied in two distance matrices [8] one intramolecular and one intermolecular. Each distance matrix describes a lower and an upper bound of the distance between every pair of atoms. Obviously, the diagonal entries of the matrices are zeroes. The intramolecular and intermolecular matrices represent the intramolecular and ....
G. M. Crippen and Timothy F. Havel. Distance geometry and molecular conformation. Chemometrics series. Wiley, 1988. 126
A Practical Clustering Algorithm for Static and Dynamic.. - Aslam, Pelekhov, Rus (1999) (1 citation) (Correct)
....distance between the clusters. approximately preserves distance relationships is required. The problem of finding such distance preserving arrangements arises in many fields, including data analysis (e.g. multidimensional scaling [KW78, CA80] and computational biology (e.g. distance geometry [CH88]) We employ techniques from distance geometry [CH88] which principally rely on eigenvalue decompositions of distance matrices, for which e#cient algorithms readily exist [PFTV88] All three views and a title window allow the user to select an individual document or a cluster. Selections made in ....
....distance relationships is required. The problem of finding such distance preserving arrangements arises in many fields, including data analysis (e.g. multidimensional scaling [KW78, CA80] and computational biology (e.g. distance geometry [CH88] We employ techniques from distance geometry [CH88] which principally rely on eigenvalue decompositions of distance matrices, for which e#cient algorithms readily exist [PFTV88] All three views and a title window allow the user to select an individual document or a cluster. Selections made in one window are simultaneously reflected in the ....
G. Crippen and T. Havel. Distance Geometry and Molecular Conformation. John Wiley & Sons Inc., 1988.
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G. M. Crippen and T.F. Havel. Distance Geometry and Molecular Conformation. Wiley, New York, 1988.
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G. M. CRIPPEN and T.F. HAVEL. Distance Geometry and Molecular Conformation. Wiley, New York, 1988.
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Crippen, G. M. and Havel, T. F. 1988. Distance Geometry and Molecular Conformation. John Wiley & Sons.
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G. M. Crippen and T. F. Havel. Distance Geometry and Molecular Conformation. John Wiley & Sons, 1988.
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Crippen, G.M. and Havel, T.F. (1988), Distance Geometry and Molecular Conformation, John Wiley & Sons, New York.
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Crippen, G.M. and Havel, T.F. (1988), Distance Geometry and Molecular Conformation, John Wiley & Sons, New York.
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Crippen, G.M. and Havel, T.F. (1988). Distance Geometry and Molecular Conformation. Wiley, New York.
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G. M. Crippen and T. F. Havel [1988]. Distance Geometry and Molecular Conformation. John Wiley & Sons, New York, NY.
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G. M. Crippen and T. F. Havel [1988]. Distance Geometry and Molecular Conformation. John Wiley & Sons, New York, NY.
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G.M. Crippen and T.F. Havel, Distance Geometry and Molecular Conformation, John Wiley & Sons, 1988.
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G. M. Crippen and T. F. Havel, Distance Geometry and Molecular Conformation, John Wiley & Sons, New York, 1988.
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Crippen G, Havel TF. "Distance Geometry and Molecular Conformation. " New York: John Wiley, 1988.
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