Topics

Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding.

08:00 EDT 24th March 2020 | BioPortfolio

Summary of "Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding."

Recent approaches to the study of biological molecules employ manifold learning to single-particle cryo-EM datasets to map the continuum of states of a molecule into a low-dimensional space spanned by eigenvectors, or "conformational coordinates". This is done separately for each projection direction (PD) on an angular grid. One important step in deriving a consolidated map of occupancies, from which the free energy landscape of the molecule can be derived, is to propagate the conformational coordinates from a given choice of "anchor PD" across the entire angular space. Even when one eigenvector dominates, its sign might invert from one PD to the next. The propagation of the second eigenvector is particularly challenging when eigenvalues of the second and third eigenvector are closely matched, leading to occasional inversions in their ranking as we move across the angular grid. In the absence of a computational approach, this propagation across the angular space has been done thus far "by hand" using visual clues, thus greatly limiting the general use of the technique. In this work we have developed a method that is able to solve the propagation problem computationally, by using optical flow and a probabilistic graphical model. We demonstrate its utility by selected examples.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of chemical information and modeling
ISSN: 1549-960X
Pages:

Links

DeepDyve research library

PubMed Articles [5504 Associated PubMed Articles listed on BioPortfolio]

Angular control of anisotropy-induced bound states in the continuum.

Radiation of leaky modes existing in anisotropic waveguides can be cancelled by destructive interference at special propagation directions relative to the optical axis orientation, resulting in fully ...

Universal momentum-to-real-space mapping of topological singularities.

Topological properties of materials are typically presented in momentum space. Here, we demonstrate a universal mapping of topological singularities from momentum to real space. By exciting Dirac-like...

Mapping data between sample and detector conjugated spaces in Bragg coherent diffraction imaging.

Bragg coherent X-ray diffraction imaging (BCDI) is a non-destructive, lensless method for 3D-resolved, nanoscale strain imaging in micro-crystals. A challenge, particularly for new users of the techni...

Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression.

Torsion angles are the natural degrees of freedom of protein structures. The ability to determine torsional variations corresponding to observed changes in Cartesian coordinates is highly valuable, no...

Capturing the dynamics of peripersonal space by integrating expectancy effects and sound propagation properties.

Humans perceive near space and far space differently. Peripersonal space (PPS), i.e. the space directly surrounding the body, is often studied using paradigms based on auditory-tactile integration. In...

Clinical Trials [1380 Associated Clinical Trials listed on BioPortfolio]

Biatrial Global High-density Electroanatomical Mapping of Atrial Fibrillation

This study uses two AcQMap imaging and electroanatomical mapping systems (Acutus Medical) to simultaneously visualise and map patterns of wavefront propagation in both the left and right a...

Probabilistic Targeting of the VIM

After having included the most improved patients by DBS among those implanted in Bordeaux Hospital University, and having defined the most active plots on tremor by its prospective grading...

Performance Evaluation of the AMS CONTINUUM™ Device

1. To assess the safety of using the CONTINUUM™ device by monitoring the side effects and complications associated with the Device following a radical prostatectomy. 2. To verify...

3D Non-invasive Myocardial Electrical Propagation Mapping as a New Tool to Predict Sudden Death Risk in Patients With Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is very common. The thickened heart muscle can disrupt the normal functioning of the heart's electrical system, resulting in fast or irregular heartbeats....

Propagation ANalysis for Arrhythmogenic Conduction Elimination to Prevent Atrial Flutter and Fibrillation (PANACEA-AF)

The purpose of this study is to perform ultra-high density mapping of the left atrium (a chamber of the heart) using the the Rhythmia Mapping System and to determine whether additional abl...

Medical and Biotech [MESH] Definitions

A statistically significant excess of cases of a disease, occurring within a limited space-time continuum.

A distribution function used to describe the occurrence of rare events or to describe the sampling distribution of isolated counts in a continuum of time or space.

Rhythmic, intermittent propagation of a fluid through a BLOOD VESSEL or piping system, in contrast to constant, smooth propagation, which produces laminar flow.

Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of immunochemistry.

Protein domains that are enriched in PROLINE. The cyclical nature of proline causes the peptide bonds it forms to have a limited degree of conformational mobility. Therefore the presence of multiple prolines in close proximity to each other can convey a distinct conformational arrangement to a peptide chain.

Quick Search


DeepDyve research library

Relevant Topic

Biological Therapy
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...


Searches Linking to this Article