Search results for "binding"
showing 10 items of 3896 documents
Dynamic-shared Pharmacophore Approach as Tool to Design New Allosteric PRC2 Inhibitors, Targeting EED Binding Pocket.
2020
Abstract: The Polycomb Repressive complex 2 (PRC2) maintains a repressive chromatin state and silences many genes, acting as methylase on histone tails. This enzyme was found overexpressed in many types of cancer. In this work, we have set up a Computer-Aided Drug Design approach based on the allosteric modulation of PRC2. In order to minimize the possible bias derived from using a single set of coordinates within the protein-ligand complex, a dynamic workflow was developed. In details, molecular dynamic was used as tool to identify the most significant ligand-protein interactions from several crystallized protein structures. The identified features were used for the creation of dynamic pha…
Single neuron binding properties and the magical number 7
2008
When we observe a scene, we can almost instantly recognize a familiar object or can quickly distinguish among objects differing by apparently minor details. Individual neurons in the medial temporal lobe of humans have been shown to be crucial for the recognition process, and they are selectively activated by different views of known individuals or objects. However, how single neurons could implement such a sparse and explicit code is unknown and almost impossible to investigate experimentally. Hippocampal CA1 pyramidal neurons could be instrumental in this process. Here, in an extensive series of simulations with realistic morphologies and active properties, we demonstrate how n radial (ob…
A Machine Learning-Based Prediction Platform for P-Glycoprotein Modulators and Its Validation by Molecular Docking
2019
P-glycoprotein (P-gp) is an important determinant of multidrug resistance (MDR) because its overexpression is associated with increased efflux of various established chemotherapy drugs in many clinically resistant and refractory tumors. This leads to insufficient therapeutic targeting of tumor populations, representing a major drawback of cancer chemotherapy. Therefore, P-gp is a target for pharmacological inhibitors to overcome MDR. In the present study, we utilized machine learning strategies to establish a model for P-gp modulators to predict whether a given compound would behave as substrate or inhibitor of P-gp. Random forest feature selection algorithm-based leave-one-out random sampl…
Temporal Binding in Multisensory and Motor-Sensory Contexts: Toward a Unified Model
2021
Our senses receive a manifold of sensory signals at any given moment in our daily lives. For a coherent and unified representation of information and precise motor control, our brain needs to temporally bind the signals emanating from a common causal event and segregate others. Traditionally, different mechanisms were proposed for the temporal binding phenomenon in multisensory and motor-sensory contexts. This paper reviews the literature on the temporal binding phenomenon in both multisensory and motor-sensory contexts and suggests future research directions for advancing the field. Moreover, by critically evaluating the recent literature, this paper suggests that common computational prin…
Density-functional tight-binding for beginners
2009
This article is a pedagogical introduction to density-functional tight-binding (DFTB) method. We derive it from the density-functional theory, give the details behind the tight-binding formalism, and give practical recipes for parametrization: how to calculate pseudo-atomic orbitals and matrix elements, and especially how to systematically fit the short-range repulsions. Our scope is neither to provide a historical review nor to make performance comparisons, but to give beginner's guide for this approximate, but in many ways invaluable, electronic structure simulation method--now freely available as an open-source software package, hotbit.
Quantum-well states in ultrathin Ag(111) films deposited onto H-passivated Si(111)-(1x1) surfaces
2002
Ag(111) films were deposited at room temperature onto H-passivated Si(111)-(1x1) substrates, and subsequently annealed at 300 C. An abrupt non-reactive Ag/Si interface is formed, and very uniform non-strained Ag(111) films of 6-12 monolayers have been grown. Angle resolved photoemission spectroscopy has been used to study the valence band electronic properties of these films. Well-defined Ag sp quantum-well states (QWS) have been observed at discrete energies between 0.5-2eV below the Fermi level, and their dispersions have been measured along the GammaK, GammaMM'and GammaL symmetry directions. QWS show a parabolic bidimensional dispersion, with in-plane effective mass of 0.38-0.50mo, along…
Computational studies of torsional properties of single-walled carbon nanotubes
2010
Current thesis presents computational studies of the torsional twist in single walled carbon nanotubes (SWCNTs). Since SWCNTs can be viewed as rolled up graphene sheets, our aim is to explain their torsion constants via shear mod- ulus of graphene in pristine, and single- and double vacancy cases. In addition, fundamental energy gap response to torsion is investigated. Calculations of defected structures is computationally expensive as it requires larger simula- tion cell with large number of atoms. To reduce the cost of computations we take the advantage of chiral symmetry of nanotubes instead of translational one, and faster performance of density-functional tight-binding method compared …
Positron trapping rate into vacancy clusters
1979
The trapping rate of positrons into vacancy clusters in metals has been calculated. It increases with the trap size and binding energy and approximately scales with the number of vacancies in small clusters. The phonon-mediated contribution to the trapping rate is small. The temperature dependence of the trapping process is discussed.
Tight-binding study of the optical properties of GaN/AlN polar and nonpolar quantum wells
2009
The electronic structure of wurtzite semiconductor superlattices (SLs) and quantum wells (QWs) is calculated by using the empirical tight-binding method. The basis used consists of four orbitals per atom (sp3 model), and the calculations include the spin-orbit coupling as well as the strain and electric polarization effects. We focus our study on GaN/AlN QWs wells grown both in polar (C) and nonpolar (A) directions. The band structure, wave functions and optical absorption spectrum are obtained and compared for both cases.
Singlet and triplet excitons in conjugated polymers.
1992
Exciton states in conjugated polymers are theoretically studied in the Su-Schrieffer-Heeger model supplemented by long-range Coulomb interactions. The relationship between exciton energies and basic interaction parameters is clarified, demonstrating the special nature of one-dimensional excitons. The binding energies of the lowest singlet and triplet excitons depend sensitively upon the on-site Coulomb energy. Relevant experiments in polydiacetylene can be explained by the present model using moderate interaction strength.