Wavelets and molecular structure

Summary The wavelet method offers possibilities for display, editing, and topological comparison of proteins at a user-specified level of detail. Wavelets are a mathematical tool that first found application in signal processing. The multiresolution analysis of a signal via wavelets provides a hierarchical series of best lower-resolution approximations. B-spline ribbons model the protein fold, with one control point per residue. Wavelet analysis sets limits on the information required to define the winding of the backbone through space, suggesting a recognizable fold is generated from a number of points equal to 1/4 or less the number of residues. Wavelets applied to surfaces and volumes show promise in structure-based drug design.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.     

A homology/ab initio hybrid algorithm for sampling near‐native protein conformations

One of the major challenges for protein tertiary structure prediction strategies is the quality of conformational sampling algorithms, which can effectively and readily search the protein fold space to generate near‐native conformations. In an effort to advance the field by making the best use of available homology as well as fold recognition approaches along with ab initio folding methods, we have developed Bhageerath‐H Strgen, a homology/ab initio hybrid algorithm for protein conformational sampling. The methodology is tested on the benchmark CASP9 dataset of 116 targets. In 93% of the cases, a structure with TM‐score ≥ 0.5 is generated in the pool of decoys. Further, the performance of Bhageerath‐H Strgen was seen to be efficient in comparison with different decoy generation methods. The algorithm is web enabled as Bhageerath‐H Strgen web tool which is made freely accessible for protein decoy generation ( http://www.scfbio‐iitd.res.in/software/Bhageerath‐HStrgen1.jsp ). © 2013 Wiley Periodicals, Inc.     

Laryngeal Hyperfunction During Whispering: Reality or Myth?

For years, otolaryngologists and voice therapists have warned voice patients that whispering causes more trauma to the larynx than normal speech. However, no large series of patients has ever been examined fiberoptically during whispering to test this hypothesis. As part of our routine examination, patients are asked to count from 1 to 10 in a normal voice and in a whispered voice. We reviewed recorded fiberoptic examinations of 100 patients who had voice complaints. We compared supraglottic hyperfunction and vocal fold closure during the normal and whispered phonation of each patient. Sixty-nine percent of the patients demonstrated increased supraglottic hyperfunction with whispered voice. Eighteen percent had no change, and 13% had less severe hyperfunction. The most common glottal configuration during whisper was an inverted Y, which resulted from compression of the anterior and middle thirds of the true vocal folds. However, 12 patients had no true vocal fold contact during whispered voice, despite having adequate glottic closure with normal voice. Although whispering involves more severe hyperfunction in most patients, it does not seem to do so in all patients. In some patients, it may be less traumatic than normal voice.     

Influence of water spraying on an oscillating channel

The influence of surface hydration on the fluid–structure instability underlying vocal folds auto-oscillation during voiced speech sound production is an open research question. In this work the influence of homogeneous water spraying on an oscillating channel is investigated experimentally using several vocal folds replicas. Changes to glottal flow features are systematically quantified for a rigid replica with forced oscillation. Changes to auto-oscillation features are systematically quantified by analyzing the pressure measured upstream from deformable replicas. During auto-oscillation it is observed for increasing water volume that the first harmonic frequency decreases, its amplitude increases, cycle-to-cycle as well as overall fluctuations increase and the closing-opening asymmetry changes. Nevertheless, the magnitude of these effects differs between deformable replicas so that further systematic investigation is needed to quantify observations as well as to explore underlying mechanisms. Flow tendencies observed on all replicas support that water spraying affects the glottal flow rather then structural properties. This is an important finding for future modeling of the effect of water spraying on the fluid–structure interaction.