Voronoi binding site models

Voronoi binding site models.

Voronoi Binding Site Models: Calculation of Binding Modes and Influence of Drug Binding Data Accuracy

A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton’s numerical metho...

Dangerous connections: on binding site models of infectious disease dynamics

We formulate models for the spread of infection on networks that are amenable to analysis in the large population limit. We distinguish three different levels: (1) binding sites, (2) individuals, and (3) the population. In the tradition of physiologically structured population models, the formulation starts on the individual level. Influences from the 'outside world' on an individual are captur...

Predicting metal-binding site residues in low-resolution structural models.

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approxim...

آنالیز پروفایل nbs (nucleotide binding-site) ژنهای مقاومت به بیماری در ارقام مختلف زیتون

به منظور مطالعه ژنهای مقاومت nbs-lrr و تنوع ژنتیکی آنها در بین ارقام بومی زیتون و همچنین مقایسه آن با ارقام خارجی، از تکنیک profiling nbs و آنالیزهای مولکولی استفاده شد. برای این منظور dna ژنومی تعداد 5 رقم خارجی و 5 رقم داخلی زیتون استخراج و با آنزیم های برشی alui و rsai هضم و با استفاده از 3 آغازگر دژنره( nbs2،nbs7،nbs5a) در دو مرحله تکثیر شدند و الگوی باندی حاصل از تکثیر انتخابی آنها در روی ...