Protein loop modeling by using fragment assembly and analytical loop closure

Protein loop modeling by using fragment assembly and analytical loop closure.

Protein loops are often involved in important biological functions such as molecular recognition, signal transduction, or enzymatic action. The three dimensional structures of loops can provide essential information for understanding molecular mechanisms behind protein functions. In this article, we develop a novel method for protein loop modeling, where the loop conformations are generated by ...

Protein Loop Prediction by Fragment Assembly

Protein Loop Closure Using Orientational Restraints from NMR Data

Protein loops often play important roles in biological functions. Modeling loops accurately is crucial to determining the functional specificity of a protein. Despite the recent progress in loop prediction approaches, which led to a number of algorithms over the past decade, few rigorous algorithmic approaches exist to model protein loops using global orientational restraints, such as those obt...

Loop-closure principles in protein folding.

Simple theoretical concepts and models have been helpful to understand the folding rates and routes of single-domain proteins. As reviewed in this article, a physical principle that appears to underly these models is loop closure.

Resultants and Loop Closure

The problem of tripeptide loop closure is formulated in terms of the angles { i}i 1 3 describing the orientation of each peptide unit about the virtual axis joining the C atoms. Imposing the constraint that at the junction of two such units the bond angle between the bonds C ON and C OC is fixed at some prescribed value results in a system of three bivariate polynomials in ui : tan i/2 of degre...