Computational techniques for efficient conformational sampling of proteins

Focused conformational sampling in proteins.

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare e...

Efficient sampling techniques for uncertainty

5 The Markov Chain Monte Carlo (MCMC) is a rigorous sampling method to quan6 tify uncertainty in subsurface characterization. However, the MCMC usually requires 7 many flow and transport simulations in evaluating the posterior distribution and can be 8 computationally expensive for fine-scale geological models. We propose a methodology 9 that combines coarseand fine-scale information to improve...

Nail Sampling techniques for Diagnosing of onychomycosis-Section 10

The clinical suspicion of onychomycosis based on appearance of the nails, requires fungal culture for confirmation. The unfamiliar terminologies used in reporting culture results leads to misinterpretation and hamper treatment decision. Accurate laboratory diagnosis of onychomycosis depends on the quality of sample collection, and reporting by microbiologist. Site selection for sampling depends...

An efficient conformational sampling method for homology modeling.

The structural refinement of protein models is a challenging problem in protein structure prediction (Moult et al., Proteins 2003;53(Suppl 6):334-339). Most attempts to refine comparative models lead to degradation rather than improvement in model quality, so most current comparative modeling procedures omit the refinement step. However, it has been shown that even in the absence of alignment e...

Enhanced Conformational Sampling of Proteins Using TEE-REX