Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Response Surface Methodology01:16

Response Surface Methodology

Response Surface Methodology (RSM) is a collection of statistical and mathematical techniques used to develop, improve, and optimize processes. It is particularly valuable when many input variables or factors potentially influence a response variable.
The process of RSM involves several key steps:
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
Surface Tension and Surface Energy01:16

Surface Tension and Surface Energy

When a paint brush is immersed in water, the bristles wave freely inside the water. When it is taken out, the bristles stick together. The reason behind this effect is surface tension.
Consider a beaker filled with liquid. The bulk molecules in the liquid experience equal attractive forces on all sides with the surrounding molecules. However, the surface molecules experience a net attractive force downward due to the bulk molecules. The surface of the liquid behaves like a stretched membrane,...
Dimensional Analysis01:23

Dimensional Analysis

Dimensional analysis is a powerful tool that is used in physics and engineering to understand and predict the behavior of physical systems. The basic idea behind dimensional analysis is to express physical quantities in terms of fundamental dimensions such as the mass, length, and time. Derived dimensions like the velocity, acceleration, and force are derived from the combinations of these fundamental dimensions.
Dimensional analysis allows us to analyze and compare physical quantities on a...
Dimensional Analysis02:19

Dimensional Analysis

The concept of dimension is important because every mathematical equation linking physical quantities must be dimensionally consistent, implying that mathematical equations must meet the following two rules. The first rule is that, in an equation, the expressions on each side of the equal sign must have the same dimensions. This is fairly intuitive since we can only add or subtract quantities of the same type (dimension). The second rule states that, in an equation, the arguments of any of the...

You might also read

Related Articles

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

Sort by
Same author

Microglial epigenetic memory is associated with accelerated resolution of inflammatory pain induced by prophylactic macrophage-derived small extracellular vesicles.

bioRxiv : the preprint server for biology·2026
Same author

Differential Gene Expression in Healing and Non-Healing Diabetic Foot Ulcers and Discovery of Novel Ratiometric Biomarker to Predict Healing Outcome.

Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society·2025
Same author

Cardiac arrest during peri-anesthetic systemic induction and maintenance in valvular heart disease: proceed or abandon? Clinical validation of a modified cardiopulmonary bypass strategy in 21 patients.

European journal of medical research·2025
Same author

Dual-functional Anti-hPSMA<sup>EC domain</sup> nanocapsules for targeted inhibition of prostate tumor growth.

Apoptosis : an international journal on programmed cell death·2025
Same author

Promoter- and enhancer-dependent cohesin loading initiates chromosome looping to fold Tcrb loci for long-range recombination.

Cell reports·2025
Same author

Reverse polarity of amide nitrogen enables expedient access to N-cyano amides.

Nature communications·2025
Same journal

To explore the molecular mechanism of IRF7 involved in acute kidney injury in sepsis based on proteomics.

Proteome science·2025
Same journal

Plasma proteome analysis of rheumatic patients reveals differences in fingerprints based on cardiovascular history: a pilot study.

Proteome science·2025
Same journal

Identification of noval diagnostic biomarker for HFpEF based on proteomics and machine learning.

Proteome science·2025
Same journal

Identification of proteome-wide and functional analysis of lysine crotonylation in multiple organs of the human fetus.

Proteome science·2025
Same journal

MiR-18a-LncRNA NONRATG-022419 pairs targeted PRG-1 regulates diabetic induced cognitive impairment by regulating NGF\BDNF-Trkb signaling pathway.

Proteome science·2025
Same journal

Metabolism-related proteins as biomarkers for predicting prognosis in polycystic ovary syndrome.

Proteome science·2024
See all related articles

Related Experiment Video

Updated: May 20, 2026

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data
09:37

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data

Published on: April 26, 2016

Protein surface representation and analysis by dimension reduction.

Heng Yang1, Rehman Qureshi, Ahmet Sacan

  • 1Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health System, Drexel University, 3120 Market Street, Philadelphia, PA 19104, USA. ahmet.sacan@drexel.edu.

Proteome Science
|July 5, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method to represent and compare protein surfaces by mapping 3-D structures to 2-D images. This approach enhances the identification of functional sites and structural similarities between proteins.

More Related Videos

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

Resolving Water, Proteins, and Lipids from In Vivo Confocal Raman Spectra of Stratum Corneum through a Chemometric Approach
09:32

Resolving Water, Proteins, and Lipids from In Vivo Confocal Raman Spectra of Stratum Corneum through a Chemometric Approach

Published on: September 26, 2019

Related Experiment Videos

Last Updated: May 20, 2026

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data
09:37

Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed Tomography Data

Published on: April 26, 2016

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps
08:59

Morphology-Based Distinction Between Healthy and Pathological Cells Utilizing Fourier Transforms and Self-Organizing Maps

Published on: October 28, 2018

Resolving Water, Proteins, and Lipids from In Vivo Confocal Raman Spectra of Stratum Corneum through a Chemometric Approach
09:32

Resolving Water, Proteins, and Lipids from In Vivo Confocal Raman Spectra of Stratum Corneum through a Chemometric Approach

Published on: September 26, 2019

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein science

Background:

  • Protein structures offer more conserved functional information than sequences.
  • Analysis of protein surfaces is crucial for understanding protein functions and interactions, but computationally challenging.
  • Existing methods may miss functional and evolutionary features by focusing solely on backbone analysis.

Purpose of the Study:

  • To develop a new computational method for representing and comparing protein surface features.
  • To enable efficient and accurate functional characterization of proteins through surface analysis.
  • To overcome the challenges in computational analysis and comparison of protein surfaces.

Main Methods:

  • Mapping 3-D protein surfaces onto 2-D maps using dimension reduction techniques.
  • Encoding geometric and biochemical features (hydrophobicity, electrostatic potential, curvature) into color channels of the 2-D map.
  • Utilizing 2-D image registration methods for comparing protein surfaces and identifying shared features.

Main Results:

  • Dimension reduction methods like SNE, LandmarkIsomap, Isomap, and Sammon's mapping effectively preserve surface properties.
  • The 2-D representation accurately characterizes functional sites, exemplified by chymotrypsin.
  • Structural similarities between proteins, such as heat shock proteins, were successfully detected.
  • A texture mapping application for protein structure visualization using the 2-D representation was proposed.

Conclusions:

  • The proposed method provides an effective way to represent and compare protein surfaces.
  • This approach enhances the ability to identify functional sites and structural similarities, aiding in protein function elucidation.
  • The 2-D mapping technique offers a valuable tool for protein structure visualization and analysis.