Related papers: Protein structure classification based on X-ray la…
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.…
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein…
Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Determining the absolute configuration of gas-phase molecules in position-space has long been a fundamental challenge in molecular physics. While strong-field-induced Coulomb explosion imaging (CEI) has emerged as a powerful tool for…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
High-energy nuclear collisions have recently emerged as a promising ``imaging-by-smashing'' approach that may reveal the intrinsic shapes of atomic nuclei. Here, I outline a conceptual framework for this technique, explaining how nuclear…
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…
Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive,…
In this paper we examine the behavior of small cluster of atoms in a short (10-50 fs) very intense hard x-ray (10 keV) pulse. We use numerical modeling based on the non-relativistic classical equation of motion. Quantum processes are taken…
Research in bioinformatics is a complex phenomenon as it overlaps two knowledge domains, namely, biological and computer sciences. This paper has tried to introduce an efficient data mining approach for classifying proteins into some useful…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
We present a simple quantum mechanical model to describe Coulomb explosion of H$_2^+$ by short, intense, infrared laser pulses. The model is based on the length gauge version of the molecular strong-field approximation and is valid for…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Intense, ultrashort pulses of 800 nm laser light (12 fs, $\sim$4 optical cycles) of peak intensity 5$\times$10$^{14}$ W cm$^{-2}$ have been used to irradiate gas-phase Xe$_n$ clusters ($n$=500-25,000) so as to induce multiple ionization and…
Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning…
The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous…
A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…