Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Geometric Mean

Geometric Mean

The mean is a measure of the central tendency of a data set. In some data sets, the data is inherently multiplicative, and the arithmetic mean is not useful. For example, the human population multiplies with time, and so does the credit amount of financial investment, as the interest compounds over successive time intervals.
In cases of multiplicative data, the geometric mean is used for statistical analysis. First, the product of all the elements is taken. Then, if there are n elements in the...

Geometric Sequences

Geometric Sequences

In systems where values diminish by a constant proportion at each stage, the resulting sequence follows a geometric structure. Each new value in the sequence is obtained by applying a fixed multiplier to the preceding term. This regular, proportional decline type is often used to represent processes involving gradual loss, such as energy dissipation or reduction in amplitude over time.When analyzing the total effect of such a process across unlimited iterations, the series of values is referred...

Oral Cavity

Oral Cavity

The oral cavity, or the mouth, is a complex structure in humans that plays a vital role in our day-to-day lives. Its role is not only in chewing and swallowing food; it also plays a role in speech and facial expressions.
Teeth: The teeth are the hardest structures in our bodies. Humans have two sets of teeth throughout their lifetime: deciduous (baby) teeth and permanent teeth. Each tooth consists of several parts: the crown (visible part), the root (embedded in the jaw), enamel (hard outer...

Trial and Error and Algorithm

Trial and Error and Algorithm

A problem-solving strategy is a plan of action used to find a solution. Different strategies have distinct action plans. Trial and error involves trying different solutions until one works. For instance, to fix a broken printer, you might check ink levels, ensure the paper tray isn't jammed, and verify the printer's connection to your laptop. This method can be time-consuming but is commonly used. Thomas Edison, for example, used trial and error to find a suitable filament for the light...

Nose and Nasal Cavity

Nose and Nasal Cavity

The nose is composed of an observable exterior segment (external nose) and an internal segment within the skull known as the nasal cavity (internal nose). The external nose, visible on the face, consists of a framework of bone and hyaline cartilage enveloped in skin and muscle and lined with a mucous membrane. This structure is supported by the frontal bone, nasal bones, and maxillary bone and is supplemented by a cartilaginous framework comprising the septal nasal cartilage, lateral nasal...

Econometric Views (EViews)

Econometric Views (EViews)

Econometric Views, often stylized as EViews, is a package that merges statistical analysis with econometric studies. It is designed to provide tools for time series analysis, forecasting, and econometric model simulation. The software originated from MicroTSP software and has evolved significantly since its inception in 1981. The history of EViews is marked by a continuous effort to enhance its computational speed and user interface. It was initially developed for large computing systems but...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

CavBench: A benchmark for protein cavity detection methods.

PloS one·2019

Same author

GPU-based detection of protein cavities using Gaussian surfaces.

BMC bioinformatics·2017

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 30, 2026

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Published on: August 31, 2022

CavVis-A Field-of-View Geometric Algorithm for Protein Cavity Detection.

Tiago M C Simões^1,2, Abel J P Gomes^1,2

¹Instituto de Telecomunicações , Delegação da Covilhã , 6200-001 Covilhã , Portugal.

Journal of Chemical Information and Modeling

|January 11, 2019

Summary

This summary is machine-generated.

This study presents CavVis, a novel computational method for identifying protein cavities. CavVis utilizes voxelization and Gaussian surfaces for accurate detection of binding sites in proteins.

More Related Videos

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Machine Learning Algorithms for Early Detection of Bone Metastases in an Experimental Rat Model

Machine Learning Algorithms for Early Detection of Bone Metastases in an Experimental Rat Model

Published on: August 16, 2020

Related Experiment Videos

Last Updated: Jan 30, 2026

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Detection and Quantification of Tunneling Nanotubes Using 3D Volume View Images

Published on: August 31, 2022

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

Machine Learning Algorithms for Early Detection of Bone Metastases in an Experimental Rat Model

Machine Learning Algorithms for Early Detection of Bone Metastases in an Experimental Rat Model

Published on: August 16, 2020

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Science

Background:

Protein cavities, or binding sites, are crucial for understanding protein-ligand interactions and protein docking.
Existing geometric methods for cavity detection have limitations.
Accurate identification of these sites is essential for drug discovery and molecular modeling.

Purpose of the Study:

To introduce CavVis, a new computational method for detecting and identifying protein cavities.
To provide an accurate and efficient tool for analyzing putative binding sites on proteins.
To enhance the study of protein-ligand interactions and protein docking.

Main Methods:

CavVis combines voxelization (a grid of voxels) with an analytic Gaussian surface formulation.
The method approximates the solvent-excluded surface.
It leverages computer graphics concepts: field-of-view, voxel ray casting, and back-face culling for cavity detection.

Main Results:

CavVis offers a novel approach to protein cavity detection.
The integration of voxelization and Gaussian surfaces provides a robust method.
Visibility criteria enhance the accuracy of identifying binding pockets.

Conclusions:

CavVis represents a significant advancement in computational methods for protein cavity analysis.
The method's reliance on visibility principles offers a unique perspective.
This tool can aid in the study of protein function and the development of targeted therapeutics.