相关论文: On the Way to More Convenient Description of Drug-…
In diffusion-controlled drug delivery, it is possible for drug molecules to bind to the carrier material and never be released. A common way to incorporate this phenomenon into the governing mechanistic model is to include an irreversible…
Time-dependent plasma codes are a natural extension of static nonequilibrium plasma codes. Comparing relevant timescales will determine whether or not time-dependent treatment is necessary. In this article I outline the ingredients for a…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
We propose a data-dependent early completion of dose finding trials for drug-combination. The early completion is determined when a beta-binomial probability for dose retainment with the trial data and the number of remaining patients is…
We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In…
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo…
Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a…
Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…
Each and every biological function in living organism happens as a result of protein-protein interactions.The diseases are no exception to this. Identifying one or more proteins for a particular disease and then designing a suitable…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…
Developing and discovering new drugs is a complex and resource-intensive endeavor that often involves substantial costs, time investment, and safety concerns. A key aspect of drug discovery involves identifying novel drug-target (DT)…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
An antiproton plasma confined in a quasi-1D device is described in terms of a self-consistent fluid formulation using a variational approach. Unlike previous treatments, the use of the time-dependent variational method allows to retain the…
In this work, the stopping power of a partially ionized plasma is analyzed by means of free electron stopping and bound electron stopping. For the first one, the RPA dielectric function is used, and for the latter one, an interpolation of…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
In a two-dimensional two-component plasma, the second moment of the density correlation function has the simple value {12 pi [1-(gamma/4)]^2}^{-1}, where gamma is the dimensionless coupling constant. This result is derived by using…
Binding free energies are a key element in understanding and predicting the strength of protein--drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs including transition metal…