Related papers: Comparative analysis of protein structure using mu…
We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.
We present in this work a new methodology to design kernels on data which is structured with smaller components, such as text, images or sequences. This methodology is a template procedure which can be applied on most kernels on measures…
This paper proposes a new mathematical framework that can be applied to biological problems such as analysis of the structures of proteins and protein complexes. In particular, it gives a new method for encoding the three-dimensional…
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…
Network theorists have developed methods to characterize the complex interactions in natural phenomena. The structure of the network of interactions between proteins is important in the field of proteomics, and has been subject to intensive…
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…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…
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…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
This paper deals with the relations among structural, topological, and chemical properties of the E.Coli proteome from the vantage point of the solubility/aggregation propensity of proteins. Each E.Coli protein is initially represented…
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…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
The present work shows a novel fractal dimension method for shape analysis. The proposed technique extracts descriptors from the shape by applying a multiscale approach to the calculus of the fractal dimension of that shape. The fractal…
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…