An important unsolved problem in structural bioinformatics is that of protein structure prediction (PSP), the reconstruction of a biologically plausible three-dimensional structure for a given protein given only its amino acid sequence. The PSP problem is of enormous interest, because the function of proteins is a direct consequence of their three-dimensional structure. Approaches to solve the ...

Clustering is a technique that aims to group data objects. Various similarity measures such as Euclidean, city-block, Mahalanobis distances and coisine similarity [1] have been used for discovering the underlying structures in data. Formally, the problem of clustering may be described as follows: Given a set of data objects X = {x1, x2, . . . , xn}, a clustering algorithm determines a suitable ...

The field of structural bioinformatics has been extensively explored in the recent years. A glance into the on-line book store Amazon.com, Inc. shows several hundred titles related to this topic. Ordering them according to the relevance gives the Burkowski's book the 2nd position. To make a profound analysis of the book and to compare it to the others published so far suggests that the reviewer...

We report here the release of a web based tool (MDDNA) to study and model the fine structural details of DNA on the basis of data extracted from a set of molecular dynamics (MD) trajectories of DNA sequences involving all the unique tetranucleotides. The dynamic web interface can be employed to analyze the first neighbor sequence context effects on the 10 unique dinucleotide steps of DNA. Funct...

The prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein consists of determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled according to their physicochemical similaritie...

Supplementary Figure S1. Parameters used for surface area and void calculations. For any two overlapping atoms i and j, various distances and angles are represented in the figure. These parameters are used in different equations shown in the main text for computation of MSA/SASA and void volume.

SUMMARY Antibodies are rapidly becoming essential tools in the clinical practice, given their ability to recognize their cognate antigens with high specificity and affinity, and a high yield at reasonable costs in model animals. Unfortunately, when administered to human patients, xenogeneic antibodies can elicit unwanted and dangerous immunogenic responses. Antibody humanization methods are des...

The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in pl...

The data management problems in grid computing are often challenging in many aspects such as data volumes, heterogeneity, structural complexity and semantic content. Thus, e-Scientists and scientific application developers stand to benefit from tools and environments that either hide, or help to manage, the inherent complexity involved in accessing and making concerted use of the diverse resour...

Structural bioinformatics of RNA has evolved mainly in response to the rapidly accumulating evidence that non-(protein)-coding RNAs (ncRNAs) play critical roles in gene regulation and development. The structures and functions of most ncRNAs are however still unknown. Most of the available RNA structural databases rely heavily on known 3D structures, and contextually correlate base pairing geome...