Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the protein structure one has to solve the Euclidean distance geometry problem given the incomplete interval distance data produced by NMR machines. In this paper, we propose a new genetic algorithm for solving the Euclidean distance geometry problem for protein structure prediction given sparse NMR data. Our genetic algorithm uses a greedy mutation operator to intensify the search, a twin removal technique for diversification in the population and a random restart method to recover stagnation. On a standard set of benchmark dataset, our algorithm significantly outperforms standard genetic algorithms.
Evolving networks of ad-hoc wireless sensing nodes rely heavily on the ability to establish position information. The algorithms presented herein rely on range measurements between pairs of nodes and the a priori coordinates of sparsely located anchor nodes. Clusters of nodes surrounding anchor nodes cooperatively establish confident position estimates through assumptions, checks, and iterative refinements. Once established, these positions are propagated to more distant nodes, allowing the entire network to create an accurate map of itself. Major obstacles include overcoming inaccuracies in range measurements as great as spl plusmn 50 , as well as the development of initial guesses for node locations in clusters with few or no anchor nodes. Solutions to these problems are presented and discussed, using position error as the primary metric. Algorithms are compared according to position error, scalability, and communication and computational requirements. Early simulations yield average position errors of 5 in the presence of both range and initial position inaccuracies. Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. The human brain confronts the same problem in everyday perception, extracting from its high-dimensional sensory inputs—30,000 auditory nerve fibers or 106 optic nerve fibers—a manageably small number of perceptually relevant features. Here we describe an approach to solving dimensionality reduction problems that uses easily measured local metric information to learn the underlying global geometry of a data set. Unlike classical techniques such as principal component analysis (PCA) and multidimensional scaling (MDS), our approach is capable of discovering the nonlinear degrees of freedom that underlie complex natural observations, such as human handwriting or images of a face under different viewing conditions. In contrast to previous algorithms for nonlinear dimensionality reduction, ours efficiently computes a globally optimal solution, and, for an important class of data manifolds, is guaranteed to converge asymptotically to the true structure. Euclidean distance geometry is the study of Euclidean geometry based on the concept of distance. This is useful in several applications where the input data consist of an incomplete set of distances and the output is a set of points in Euclidean space realizing those given distances. We survey the theory of Euclidean distance geometry and its most important applications, with special emphasis on molecular conformation problems. We study the performance of the code for the solution of distance geometry problems with lower and upper bounds on distance constraints. The code uses only a sparse set of distance constraints, while other algorithms tend to work with a dense set of constraints either by imposing additional bounds or by deducing bounds from the given bounds. Our computational results show that protein structures can be determined by solving a distance geometry problem with and that the approach based on is significantly more reliable and efficient than multi-starts with an optimization code. Distance geometry problems arise in the determination of protein structure. We consider the case where only a subset of the distances between atoms is given and formulate this distance geometry problem as a global minimization problem with special structure. We show that global smoothing techniques and a continuation approach for global optimization can be used to determine global solutions of this problem reliably and efficiently. The global continuation approach determines a global solution with less computational effort than is required by a standard multistart algorithm. Moreover, the continuation approach usually finds the global solution from any given starting point, while the multistart algorithm tends to fail. In this paper we develop a set of inverse kinematics algorithms suitable for an anthropomorphic arm or leg. We use a combination of analytical and numerical methods to solve generalized inverse kinematics problems including position, orientation, and aiming constraints. Our combination of analytical and numerical methods results in faster and more reliable algorithms than conventional inverse Jacobian and optimization-based techniques. Additionally, unlike conventional numerical algorithms, our methods allow the user to interactively explore all possible solutions using an intuitive set of parameters that define the redundancy of the system.  Nuclear magnetic resonance (NMR) structure modeling usually produces a sparse set of inter-atomic distances in protein. In order to calculate the three-dimensional structure of protein, current approaches need to estimate all other missing'' distances to build a full set of distances. However, the estimation step is costly and prone to introducing errors. In this report, we describe a geometric build-up algorithm for solving protein structure by using only a sparse set of inter-atomic distances. Such a sparse set of distances can be obtained by combining NMR data with our knowledge on certain bond lengths and bond angles. It can also include confident estimations on some missing'' distances. Our algorithm utilizes a simple geometric relationship between coordinates and distances. The coordinates for each atom are calculated by using the coordinates of previously determined atoms and their distances. We have implemented the algorithm and tested it on several proteins. Our results showed that our algorithm successfully determined the protein structures with sparse sets of distances. Therefore, our algorithm reduces the need of estimating the missing'' distances and promises a more efficient approach to NMR structure modeling.