The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
It is clear that the function of ion channels must flow from their structure. With recent advances in computational power and methodology, it appears feasible to correlate structure to ion channel permeation at an atomistically detailed level of description. The overall strategy is to structure the calculations in a hierarchy, ranging from coarse-grained thermodynamic and kinetic descriptions to fine-grained...
This work describes theab initioprocedure employed to build an activation model for the α 1b -adrenergic receptor (α 1b -AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and...
A three-dimensional (3D) stereoelectronic pharmacophore developed from a 3D quantitative structure–activity relationship (QSAR) investigation formed the basis of the development of a two-phase data-mining methodology to uncover novel leads to inhibit human immunodeficiency virus type 1 (HIV-1) reverse transcriptase at the nonnucleoside binding site. The database searching phase employed a field search...
Computational chemistry and molecular modeling procedures allow us to define and computead hocsize and shape descriptors on the different prototropic forms assumed by drugs in biotest solutions. Together with experimental data measured on a well-identified target receptor, these descriptors are essential elements for obtaining simple, consistent, comparable, and easily interpretable theoretical quantitative...
The DNA-binding properties of many ligands can be rationalized on the basis of their structural and electronic complementarity with the functional groups present in the minor and major grooves of particular DNA sequences. Specific hydrogen bonding patterns are particularly useful for the purpose of sequence recognition. Less obvious, however, is the influence of base composition on the conformational...
Quantitative modeling methods, relating aspects of chemical structure to biological activity, have long been applied to the prediction and characterization of chemical toxicity. The early linear free-energy approaches of Hansch and Free Wilson provided a fundamental scientific framework for the quantitative correlation of chemical structure with biological activity and spurred many developments in...
Protein association events are ubiquitous in biological systems. Some protein associations and subsequent responses are diffusion controlledin vivo.Hence, it is important to be able to compute bimolecular diffusional association rates for proteins. The Brownian dynamics simulation methodology may be used to simulate protein–protein encounter, compute association rates, and examine their dependence...
Application of the “essential dynamics” method to the NMR cluster of structures for the R2R3 DNA-binding domain of the mouse c-Myb transcriptional activator is described. Using this method, large concerted fluctuations of atoms are extracted showing a hinge-bending motion between the two (R2 and R3) Myb repeats on the basis of NMR data alone. Molecular dynamics simulation of the same protein allowed...
The field of protein structure prediction is evolving rapidly and in the last few years a number of new methods have been developed and evaluated. However, comparative modeling, or modeling by homology, is still the method of choice when the unknown protein shares any significant sequence similarity with a protein of known structure. The accuracy of the method is highly dependent on the degree of...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.