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Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
By performing high-throughput first-principles calculations combined with a semiempirical van der Waals dispersion correction, we have screened 74 direct- and 185 indirect-gap two dimensional (2D) nonmagnetic semiconductors from near 1000…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…
This paper is devoted to the problem of identification of colloidal assemblies using the example of two-dimensional coatings (monolayer assemblies). Colloidal systems are used in various fields of science and technology, for example, in…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
Instead of conformation states of single residues, refined conformation states of quintuplets are proposed to reflect conformation correlation. Simple hidden Markov models combining with sliding window scores are used for predicting…
Multivariate normal mixtures provide a flexible method of fitting high-dimensional data. It is shown that their topography, in the sense of their key features as a density, can be analyzed rigorously in lower dimensions by use of a…
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.…
Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
Data-driven decompositions are becoming essential tools in fluid dynamics, allowing for tracking the evolution of coherent patterns in large datasets, and for constructing low order models of complex phenomena. In this work, we analyze the…
Connectedness percolation phenomena in the two-dimensional (2D) packing of binary mixtures of disks with different diameters were studied numerically. The packings were produced using random sequential adsorption (RSA) model with…
Direct Coupling Analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to…
In this paper, we propose a improved 2D-PEH based on double prediction-error. First,different from previous 2D-PEH, the proposed 2D-DPEH is established by selecting two distinct predictors with low correlation to calculate double prediction…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
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…
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially…