Related papers: HBAT 2: A Python Package to Analyse Hydrogen Bonds…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of…
The Ramachandran plot is a potent way to understand structures of biomolecules, however, the original formulation of the Ramachandran plot only considers backbone conformations. We formulate a new interpretation of the original Ramachandran…
Determining potential abilities of nanostructures to induce toxicity to biological molecules is still a convoluted challenge in the realm of nanomedicine. Based on the unprecedented achievements of twodimensional nanomaterials in nearly all…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because…
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer protein chains…
The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent X-ray absorption studies. The analysis is based on ab initio molecular-dynamics…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or…
The electrostatic, entropic and surface interactions between a macroion (nanoparticle or biomolecule), surrounding ions and water molecules play a fundamental role in the behavior and function of colloidal systems. However, the molecular…
The Hofstadter model successfully describes the behavior of non-interacting quantum particles hopping on a lattice coupled to a gauge field, and hence is ubiquitous in many fields of research, including condensed matter, optical, and atomic…
The availability of accurate computational tools for modeling and simulation is vital to accelerate the discovery of materials capable of storing hydrogen (H2) under given parameters of pressure swing and temperature. Previously, we…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Efficient and high capacity storage materials are indispensable for a hydrogen-based economy. In silico tools can accelerate the process of discovery of new adsorbent materials with optimal hydrogen adsorption enthalpies. Density functional…
The properties of the hydrogen bonds in ethylammonium nitrate are analyzed by using molecular dynamics simulations and infrared as well as nuclear magnetic resonance experiments. Ethylammonium nitrate features a flexible three-dimensional…
It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Classical molecular simulation and statistical mechanics methods typically assume pairwise…
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without…
This is the manual for the version 2 of HackAnalysis, a powerful, lightweight, versatile and, most importantly, hackable, recasting tool. New features in this version include: compressed event format storage for ultra-fast development;…