Related papers: Multiple alignment of structures using center of p…
Many real-world networks exhibit a multicores-periphery structure, with densely connected vertices in multiple cores surrounded by a general periphery of sparsely connected vertices. Identification of the multicores-periphery structure can…
Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
In this PhD thesis, a novel method to determine protein structures using chemical shifts is presented.
Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
In this paper we design and analyze algorithms for asynchronously solving linear programs using nonlinear signal processing structures. In particular, we discuss a general procedure for generating these structures such that a fixed-point of…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Multi-attributed graph matching is a problem of finding correspondences between two sets of data while considering their complex properties described in multiple attributes. However, the information of multiple attributes is likely to be…
Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
A learning algorithm for multilayer perceptrons is presented which is based on finding the principal components of a correlation matrix computed from the example inputs and their target outputs. For large networks our procedure needs far…
We address the problem of recovering multiple structures of different classes in a dataset contaminated by noise and outliers. In particular, we consider geometric structures defined by a mixture of underlying parametric models (e.g. planes…
A multimodal network encodes relationships between the same set of nodes in multiple settings, and network alignment is a powerful tool for transferring information and insight between a pair of networks. We propose a method for multimodal…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
The current computer architecture has moved towards the multi/many-core structure. However, the algorithms in the current sequential dense numerical linear algebra libraries (e.g. LAPACK) do not parallelize well on multi/many-core…