Related papers: Prediction of Structures and Interactions from Gen…

Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure…

Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…

Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional…

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…

Multiple sequence alignment (MSA) data play a crucial role in the study of protein mutations, with contact prediction being a notable application. Existing methods are often model-based or algorithmic and typically do not incorporate…

Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree…

Protein structure prediction has been a grand challenge problem in the structure biology over the last few decades. Protein quality assessment plays a very important role in protein structure prediction. In the paper, we propose a new…

Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure,…

High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…

We discuss a stochastic approach for reconstructing the native structures of proteins from the knowledge of the "effective connectivity", which is a one-dimensional structural profile constructed as a linear combination of the eigenvectors…

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…

Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via…

The computational prediction of a protein structure from its sequence generally relies on a method to assess the quality of protein models. Most assessment methods rank candidate models using heavily engineered structural features, defined…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…

RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…