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Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
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…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
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…
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for…
Systematic identification of protein function is a key problem in current biology. Most traditional methods fail to identify functionally equivalent proteins if they lack similar sequences, structural data or extensive manual annotations.…
The performance and ease of use of deep learning-based binary classifiers have improved significantly in recent years. This has opened up the potential for automating critical inspection tasks, which have traditionally only been trusted to…
Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and…
Subcellular localization is a crucial biological task for drug target identification and function annotation. Although it has been biologically realized that subcellular localization is closely associated with protein structure, no existing…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
Experimental determination of protein function is resource-consuming. As an alternative, computational prediction of protein function has received attention. In this context, protein structural classification (PSC) can help, by allowing for…
Much scientific enquiry across disciplines is founded upon a mechanistic treatment of dynamic systems that ties form to function. A highly visible instance of this is in molecular biology, where an important goal is to determine…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
Research in bioinformatics is a complex phenomenon as it overlaps two knowledge domains, namely, biological and computer sciences. This paper has tried to introduce an efficient data mining approach for classifying proteins into some useful…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…