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Finding interesting phenomena is the core of scientific discovery, but it is a manual, ill-defined concept. We present an integrative pipeline for automating the discovery of interesting simple hypotheses (feature-target relations with…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Because of their large size and widespread mechanosensitive interactions the only recently discovered titled transmembrane proteins have attracted much attention. Here we present and discuss their hydropathic profiles using a new method of…
Understanding the physical and chemical properties of aqueous interfaces is important in diverse fields of science, ranging from biology and chemistry to materials science. In spite of crucial progress in surface sensitive spectroscopic…
Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++,…
The optomechanical character of molecules was discovered by Raman about one century ago. Today, molecules are promising contenders for high-performance quantum optomechanical platforms because their small size and large energy-level…
Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…
Small Ubiquitin-related modifier (SUMO) proteins are widely expressed in eukaryotic cells, which are reversibly coupled to their substrates by motif recognition, called sumoylation. Two interesting questions are 1) how many potential SUMO…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
The problem of deciphering how low-level patterns (action potentials in the brain, amino acids in a protein, etc.) drive high-level biological features (sensorimotor behavior, enzymatic function) represents the central challenge of…
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodelling cell membranes. However, the molecular driving forces behind these processes are not well…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
The ABC (ATP Binding Cassette) transporter protein superfamily comprises a large number of ubiquitous and functionally versatile proteins conserved from archaea to humans. ABC transporters have a key role in many human diseases and also in…
The native three dimensional structure of a single protein is determined by the physico chemical nature of its constituent amino acids. The twenty different types of amino acids, depending on their physico chemical properties, can be…
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically…
Ab initio calculations play an essential role in our fundamental understanding of quantum many-body systems across many subfields, from strongly correlated fermions to quantum chemistry and from atomic and molecular systems to nuclear…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
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…