Related papers: CSA: Comprehensive comparison of pairwise protein …
A new method for the Automated Protein Structure Analysis (APSA) is derived, which simplifies the protein backbone to a smooth curve in 3-dimensional space. For the purpose of obtaining this smooth line each amino acid is represented by its…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
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…
Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed "sectors". The method applies spectral analysis to a matrix obtained by combining…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…
Canonical correlation analysis (CCA) is a technique for finding correlated sets of features between two datasets. In this paper, we propose a novel extension of CCA to the online, streaming data setting: Sliding Window Informative Canonical…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult…
Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in…
The similarity in the three-dimensional structures of homologous proteins imposes strong constraints on their sequence variability. It has long been suggested that the resulting correlations among amino acid compositions at different…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
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…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
This article introduces a novel protein structure alignment method (named TALI) based on the protein backbone torsion angle instead of the more traditional distance matrix. Because the structural alignment of the two proteins is based on…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…