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The functionality of protein-protein complexes is closely tied to the strength of their interactions, making the evaluation of binding affinity a central focus in structural biology. However, the molecular determinants underlying binding…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…
In this Communication we present statistical analysis of conservation profiles in families of homologous sequences for nine proteins whose folding nucleus was determined by protein engineering methods. We show that in all but one protein…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Emerging neuroimaging evidence shows that pathological tau proteins build up along specific brain networks, suggesting that large-scale network architecture plays a key role in the progression of Alzheimer's disease (AD). However, how…
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of…
Protein aggregation is an important field of investigation because it is closely related to the problem of neurodegenerative diseases, to the development of biomaterials, and to the growth of cellular structures such as cyto-skeleton.…
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…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin…
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…
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…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative…
We used redescription mining to find interpretable rules revealing associations between those determinants that provide insights about the Alzheimer's disease (AD). We extended the CLUS-RM redescription mining algorithm to a…
Predicting the functional impact of single amino acid substitutions (SAVs) is central to understanding genetic disease and engineering therapeutic proteins. While protein language models and structure-based methods have achieved strong…