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

Fischer Projections

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...

Newman Projections

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...

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Dynamics in Living Cells

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

You might also read

Related Articles

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

Sort by

Same author

FOXM1-Specific TCR-Engineered T Cells Target Non-Small Cell Lung Cancer.

Cancer immunology research·2026

Same author

STEGG: Structural TCR-pMHC ensemble generator and gallery.

Journal of molecular biology·2026

Same author

STAG-LLM: Predicting TCR-pHLA binding with protein language models and computationally generated 3D structures.

Computational and structural biotechnology journal·2026

Same author

TCR-pMHC Binding Specificity Prediction From Structure Using Graph Neural Networks.

IEEE transactions on computational biology and bioinformatics·2025

Same author

DINC-ensemble: A web server for docking large ligands incrementally to an ensemble of receptor conformations.

Journal of molecular biology·2025

Same author

MoleQCage: Geometric High-Throughput Screening for Molecular Caging Prediction.

Journal of chemical information and modeling·2024

Search research articles

Related Experiment Video

Updated: Mar 11, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Defining Low-Dimensional Projections to Guide Protein Conformational Sampling.

Anastasia Novinskaya¹, Didier Devaurs¹, Mark Moll¹

¹Department of Computer Science, Rice University , Houston, Texas.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|November 29, 2016

Summary

This summary is machine-generated.

This study introduces novel low-dimensional projections to improve protein conformational sampling using robotics-inspired algorithms. Both expert-guided and automated methods enhance exploration of protein structures and functions.

Keywords:

low-dimensional projection protein conformational sampling protein flexibility sampling-based planning.

More Related Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Mar 11, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Computational Biology
Robotics
Structural Bioinformatics

Background:

Protein conformational space exploration is crucial for understanding protein function.
Sampling-based motion-planning algorithms are effective but face the curse of dimensionality for large proteins.
Low-dimensional projections are used to mitigate dimensionality but their selection and impact are unclear.

Purpose of the Study:

To introduce two methodologies for defining low-dimensional projections for sampling-based protein conformational sampling.
To evaluate the effectiveness of these projection methodologies in guiding conformational sampling.

Main Methods:

Developed two methodologies for constructing low-dimensional projections for protein conformational sampling.
Method 1: Leverages protein flexibility information with expert knowledge.
Method 2: Automatically constructs projections without expert intervention.

Main Results:

Projections based on expert knowledge can significantly benefit conformational sampling.
Automatically constructed projections offer a viable and effective alternative.
Evaluated methodologies on conformational search problems for three middle-size proteins.

Conclusions:

Low-dimensional projections are valuable for enhancing sampling-based protein conformational sampling.
Both expert-guided and automated projection methods demonstrate efficacy.
Automated projection construction presents a practical approach for broader application.