Biomolecules
In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction $\phi \approx 0.56$, which is the same as dense, random packing of amino…
Shape had been intuitively recognized to play a dominant role in determining the global motion patterns of bio-molecular assemblies. However, it is not clear exactly how shape determines the motion patterns. What about the local…
Unsupervised clustering has broad applications in data stratification, pattern investigation and new discovery beyond existing knowledge. In particular, clustering of bioactive molecules facilitates chemical space mapping,…
Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance,…
G protein-coupled receptors (GPCRs) are a large superfamily of membrane proteins that are activated by extracellular small molecules or photons. Neurotensin receptor 1 (NTSR1) is a GPCR that is activated by neurotensin, i.e. a 13 amino acid…
Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized…
Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous…
The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that can be expressed in HEK293T cells by stable transfection. Its ligand is a 13-amino-acid peptide that binds with nanomolar affinity from the extracellular side to…
We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer,…
Electrical signaling via voltage-gated ion channels depends upon the function of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K+ channels. Here we investigate some energetic aspects of the sliding-helix model of…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Since the largest 2014-2016 Ebola virus disease outbreak in West Africa, understanding of Ebola virus infection has improved, notably the involvement of innate immune mediators. Amongst them, collectins are important players in the…
Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships…
Many instances of cellular signaling and transcriptional regulation involve switch-like molecular responses to the presence or absence of input ligands. To understand how these responses come about and how they can be harnessed, we develop…
Direct comparison of three-dimensional (3D) objects is computationally expensive due to the need for translation, rotation, and scaling of the objects to evaluate their similarity. In applications of 3D object comparison, often identifying…
Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative…
Herein (the first part of my work), I debunk the long-standing hypotheses that explain mitochondrial oxidative phosphorylation. Simple calculations point out that mitochondria are highly proton-deficient microcosms and therefore, elaborate…