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

Protein Organization01:24

Protein Organization

8.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
8.5K
Protein Folding01:22

Protein Folding

124.8K
Overview
124.8K
Protein Folding01:25

Protein Folding

10.2K
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...
10.2K
Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

1.5K
Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
1.5K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.2K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.2K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.7K

You might also read

Related Articles

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

Sort by
Same author

Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa.

Nucleic acids research·2024
Same author

Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.

Protein science : a publication of the Protein Society·2024
Same author

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.

PLoS computational biology·2024
Same author

Simultaneous enhancement of multiple functional properties using evolution-informed protein design.

Nature communications·2024
Same author

EGGNet, a Generalizable Geometric Deep Learning Framework for Protein Complex Pose Scoring.

ACS omega·2024
Same author

Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in <i>Pseudomonas aeruginosa</i>.

bioRxiv : the preprint server for biology·2024
Same journal

Tomogram exploration through template matching and deep learning.

Current opinion in structural biology·2026
Same journal

A comparative review of cryo-electron ptychography: Biological applications and future perspectives.

Current opinion in structural biology·2026
Same journal

Metabolic disruptions through a three-dimensional genomic lens.

Current opinion in structural biology·2026
Same journal

Collective variable design for biomolecular conformational dynamics.

Current opinion in structural biology·2026
Same journal

Polymer scaling in protein crowding: From dilute coils to semidilute meshes.

Current opinion in structural biology·2026
Same journal

Tuning the physicochemical properties of rationally designed protein-based biomolecular condensates.

Current opinion in structural biology·2026
See all related articles

Related Experiment Video

Updated: Nov 27, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.3K

Toward complete rational control over protein structure and function through computational design.

Jared Adolf-Bryfogle1, Frank D Teets1, Christopher D Bahl1

  • 1Institute for Protein Innovation, Boston, MA 02115, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

Current Opinion in Structural Biology
|December 4, 2020
PubMed
Summary
This summary is machine-generated.

Developing a general method for protein design remains a grand challenge. Current approaches improve native proteins or design new ones, showing promise for arbitrary polypeptide manipulation.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

682
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

7.5K

Related Experiment Videos

Last Updated: Nov 27, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.3K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

682
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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

Published on: July 14, 2015

7.5K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Biology

Background:

  • The design of polypeptides with specific functions, conformations, and properties is a significant challenge in molecular biology.
  • Existing methods focus on improving native proteins, de novo design, and redesigning suboptimal proteins.

Purpose of the Study:

  • To explore current methodologies and assess the progress towards a general method for arbitrary polypeptide manipulation.
  • To identify the limitations and future directions in protein design.

Main Methods:

  • Informatic comparisons of protein function-structure-sequence relationships.
  • Knowledge-based evaluation of protein properties.
  • Narrowing the protein sequence search space using computational and manual methods.

Main Results:

  • A variety of methods have been developed for protein improvement and de novo design.
  • These methods effectively reduce the search space for protein sequences.
  • While arbitrary manipulation of interfaces and catalysis remains unsolved, progress indicates a general approach is attainable.

Conclusions:

  • Current protein design strategies show significant promise for achieving arbitrary polypeptide manipulation.
  • Further research is needed to address unsolved problems like interface manipulation and molecular catalysis.
  • A universal algorithm for protein shape and behavior manipulation is not yet available but is a reachable goal.