Related papers: Rigidity analysis of HIV-1 protease
The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray…
Recent interest for the development of high-temperature gas reactors has increased the need for more advanced understanding of flow characteristics in randomly packed pebble beds. A proper understanding of these flow characteristics can…
We use an elastic rod model with contact to study the extension versus rotation diagrams of single supercoiled DNA molecules. We reproduce quantitatively the supercoiling response of overtwisted DNA and, using experimental data, we get an…
We probe the dynamic strength of multiple biotin-streptavidin adhesion bonds under linear loading using the biomembrane force probe setup for dynamic force spectroscopy. Measured rupture force histograms are compared to results from a…
The influenza/H1N1 virus has caused hazard in the public health of many countries. Hence, existing influenza drugs could not cope with H1N1 infection due to the high mutation rate of the virus. In this respect, new method to block the virus…
An adhesively stressed thin film of a soft hydrogel confined between two rigid flat substrates auto-roughens with its dominant wavelength exhibiting pronounced dependence on the film thickness (H). A linear stability analysis confirmed that…
The role of fixed degrees of freedom in soft/granular matter systems has broad applicability and theoretical interest. Here we address questions of the geometrical role that a scaffolding of fixed particles plays in tuning the threshold…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
Quasi-one-dimensional (1D) materials provide a unique platform for understanding the importance and influence of extended interactions on the physics of strongly correlated systems due to their relative structural simplicity and the…
Mathematical modeling of biological systems is crucial to effectively and efficiently developing treatments for medical conditions that plague humanity. Often, systems of ordinary differential equations are a traditional tool used to…
The intricate pattern of chemical modifications on DNA and histones, the "histone code", is considered to be a key gene regulation factor. Multivalency is seen by many as an essential instrument to transmit the "encoded" information to the…
This study is concerned with behaviour of fluid of monoclonal antibodies (mAbs) when trapped in a confinement represented by rigid spherical obstacles that attract proteins. The antibody molecule is depicted as an assembly of seven hard…
Motivated by the diversity and complexity of two-dimensional crystals formed by triangular proteins and protein trimers, we have investigated the structures and phase behavior of hard-disk trimers. In order to mimic specific binding…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
The use of generative machine learning models, trained on the experimentally resolved structures deposited in the protein data bank, is an attractive approach to sampling conformational ensembles of proteins. However, the ensembles…
Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance - yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment…
The geometric optimization of crystal structures is a procedure widely used in Chemistry that changes the geometrical placement of the particles inside a structure. It is called structural relaxation and constitutes a local minimization…
Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer.…