Related papers: Rigidity analysis of HIV-1 protease
A homeomorphically irreducible spanning tree (HIST) is a spanning tree with no degree-2 vertices, serving as a structurally minimal backbone of a graph. While the existence of HISTs has been widely studied from a structural perspective, the…
Helical objects are often implemented in electronic or mechanical micro-systems, requiring a precise understanding of their mechanical properties. While helices formed by cylindrical filaments have been intensely investigated, little is…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to…
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…
Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein…
We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…
We report the reproducible first-principles folding of the 40 amino acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy forcefield. Six of twenty simulations using an adapted basin-hopping…
We present preliminary results that quantify network robustness and fragility of Ewing sarcoma (ES), a rare pediatric bone cancer that often exhibits de novo or acquired drug resistance. By identifying novel proteins or pathways susceptible…
HIV dynamic studies have contributed significantly to the understanding of HIV pathogenesis and antiviral treatment strategies for AIDS patients. Establishing the relationship of virologic responses with clinical factors and covariates…
Protein-nucleic acid complexes are important for many cellular processes including the most essential function such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown…
Rigidity percolation provides an important basis for understanding the onset of mechanical stability in disordered materials. While most studies on the triangular lattice have focused on static properties at fixed bond~(site) occupation…
We present a refined and improved study of the influence of screening on the effective fine structure constant of graphene, $\alpha^*$, as measured in graphite using inelastic x-ray scattering. This follow-up to our previous study [J. P.…
With the launch of second line anti-retroviral therapy for HIV infected individuals, there has been an increased expectation on surviving period of people with HIV. We consider previously well-known models in HIV epidemiology where the…
Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force…
We review and compare the reconstruction methods of the inclusive deep inelastic scattering variables used at HERA. We introduce a new prescription, the $\Sigma$ method, which allows to measure the structure function of the proton…
Because different patients may response quite differently to the same drug or treatment, there is increasing interest in discovering individualized treatment rule. In particular, people are eager to find the optimal individualized treatment…
The H1 and Zeus collaborations have measured the inclusive diffractive DIS cross section ep -> eXp and these measurements are in good agreement within a normalisation uncertainty. Diffractive parton density functions (DPDFs) have been…