378133
LFM-Pro: a tool for detecting significant local structural sites in proteins
MOTIVATION
The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.


RESULTS
We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.


AVAILABILITY
The software and the datasets are freely available for academic research use at http://bioinfo.ceng.metu.edu.tr/Pub/LFMPro.
2273352
Near-Linear Time Approximation Algorithms for Curve Simplification
AbstractWe consider the problem of approximating a polygonal
 curve P under a given error criterion by another
 polygonal curve P’ whose vertices are a
 subset of the vertices of P. The goal is to minimize
 the number of vertices of P’ while ensuring that the
 error between P’ and P is below a certain threshold.
 We consider two different error measures: 
 Hausdorff and Frechet. For both error criteria, we present
 near-linear time approximation algorithms that, given a
 parameter ε > 0, compute a simplified polygonal
 curve P’ whose error is less than ε and
 size at most the size of an optimal simplified
 polygonal curve with error ε/2. We consider
 monotone curves in ℝ2 in the case of the Hausdorff error measure
 under the uniform distance metric
 and arbitrary curves in any dimension for the Frechet error measure
 under Lp metrics. 
 We present
 experimental results demonstrating that our algorithms
 are simple and fast, and produce close to optimal
 simplifications in practice.
2472095
Coarse and Reliable Geometric Alignment for Protein Docking
We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.
312809
Segmenting molecular surfaces
This paper presents a new method for segmentation of molecular surfaces. Topological analysis of a scalar function defined on the surface and its associated gradient field reveals the relationship between the features of interest and critical points of the scalar function. The segmentation is obtained by associating segments with local minima/maxima. Controlled simplification of the function merges segments resulting in a hierarchical segmentation of the molecular surface. This segmentation is used to identify rigid components of protein molecules and to study the role of cavities and protrusions in protein-protein interactions.
34251654
Near-Linear Time Approximation Algorithms for Curve Simplification
We consider the problem of approximating a polygonal curve P under a given error criterion by another polygonal curve P? whose vertices are a subset of the vertices of P. The goal is to minimize the number of vertices of P? while ensuring that the error between P? and P is below a certain threshold. We consider two fundamentally different error measures -- Hausdorff and Frechet error measures. For both error criteria, we present near-linear time approximation algorithms that, given a parameter ? > 0, compute a simplified polygonal curve P? whose error is less than ? and size at most the size of an optimal simplified polygonal curve with error ?/2. We consider monotone curves in the case of Hausdorff error measure and arbitrary curves for the Frechet error measure. We present experimental results demonstrating that our algorithms are simple and fast, and produce close to optimal simplifications in practice.
7211983
Theoretical Analysis for Communication-Induced Checkpointing Protocols with Rollback-Dependency Trackability
Rollback-Dependency Trackability (RDT) is a property that states that all rollback dependencies between local checkpoints are on-line trackable by using a transitive dependency vector. In this paper, we address three fundamental issues in the design of communication-induced checkpointing protocols that ensure RDT. First, we prove that the following intuition commonly assumed in the literature is in fact false: If a protocol forces a checkpoint only at a stronger condition, then it must take, at most, as many forced checkpoints as a protocol based on a weaker condition. This result implies that the common approach of sharpening the checkpoint-inducing condition by piggybacking more control information on each message may not always yield a more efficient protocol. Next, we prove that there is no optimal on-line RDT protocol that takes fewer forced checkpoints than any other RDT protocol for all possible communication patterns. Finally, since comparing checkpoint-inducing conditions is not sufficient for comparing protocol performance, we present some formal techniques for comparing the performance of several existing RDT protocols.
8204880
Privacy aware data generation for testing database applications
Testing of database applications is of great importance. A significant issue in database application testing consists in the availability of representative data. In this paper, we investigate the problem of generating a synthetic database based on a-priori knowledge about a production database. Our approach is to fit general location model using various characteristics (e.g., constraints, statistics, rules) extracted from the production database and then generate the synthetic data using model learnt. The generated data is valid and similar to real data in terms of statistical distribution, hence it can be used for functional and performance testing. As characteristics extracted may contain information which may be used by attacker to derive some confidential information about individuals, we present our disclosure analysis method which applies cell suppression technique for identity disclosure analysis and perturbation for value disclosure.
793367
3D Brain surface matching based on geodesics and local geometry
The non-rigid registration of surfaces is a complex and difficult task for which there are many important applications, such as comparing shape between deformable objects and comparing associated function. This paper presents a new approach for brain surface matching by determining the correspondence of 3D point sets between pairs of surfaces. The algorithm is based on shape using a combination of geodesic distance and surface curvature. There are two major procedures involved. An initial sparse set of corresponding points is first generated by matching local geometrical features. Geodesic distance interpolation is then employed hierarchically in order to capture the complex surface. By this scheme, surface correspondence and triangulation are computed simultaneously. Experiments applied to human cerebral cortical surfaces are shown to evaluate the approach. It is shown that the proposed method performs well for both surface matching and surface shape recovery.
8818017
Using Model Trees for Classification
Model trees, which are a type of decision tree with linear regression functions at the leaves, form the basis of a recent successful technique for predicting continuous numeric values. They can be applied to classification problems by employing a standard method of transforming a classification problem into a problem of function approximation. Surprisingly, using this simple transformation the model tree inducer M5′, based on Quinlan's M5, generates more accurate classifiers than the state-of-the-art decision tree learner C5.0, particularly when most of the attributes are numeric.
28934685
Unsupervised Bilingual Word Sense Disambiguation Using Web Statistics
Word sense disambiguation has sense division and sense selection as its two sub-problems. An appropriate solution to the sense division problem is usually dependent on the application being pursued. In the context of machine translation, picking the correct translation for a word among multiple candidates, is known as target word selection. 
 
The work in this paper uses the Web as the main knowledge source to address the difficulty of making a target word selection based on statistics, which are normally drawn from rather limited corpora. The proposed approach uses simple and easily accessible web statistics–search engine hits (number of document returned for a particular query) to demonstrate the great potential of the Web as a knowledge source for word sense disambiguation. Our experimental results so far are very encouraging.