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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…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…
A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and proteomics) have…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Recent computational advances in the accurate prediction of protein three-dimensional (3D) structures from amino acid sequences now present a unique opportunity to decipher the interrelationships between proteins. This task entails--but is…
Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for…
This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…
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…
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…
As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed for rapid screening, but there…
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…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…