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

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein Organization01:24

Protein Organization

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.
Protein Organization01:24

Protein Organization

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.
Protein Organization01:13

Protein Organization

Overview
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

You might also read

Related Articles

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

Sort by
Same author

Discovery of BMS-986339, a Pharmacologically Differentiated Farnesoid X Receptor Agonist for the Treatment of Nonalcoholic Steatohepatitis.

Journal of medicinal chemistry·2022
Same author

Discovery of a Partial Glucokinase Activator Clinical Candidate: Diethyl ((3-(3-((5-(Azetidine-1-carbonyl)pyrazin-2-yl)oxy)-5-isopropoxybenzamido)-1<i>H</i>-pyrazol-1-yl)methyl)phosphonate (BMS-820132).

Journal of medicinal chemistry·2022
Same author

Design for Solubility May Reveal Induction of Amide Hydrogen/Deuterium Exchange by Protein Self-Association.

Journal of molecular biology·2021
Same author

Identification of a Hydroxypyrimidinone Compound (<b>21</b>) as a Potent APJ Receptor Agonist for the Potential Treatment of Heart Failure.

Journal of medicinal chemistry·2021
Same author

Discovery of BMS-986318, a Potent Nonbile Acid FXR Agonist for the Treatment of Nonalcoholic Steatohepatitis.

ACS medicinal chemistry letters·2021
Same author

Discovery of Milvexian, a High-Affinity, Orally Bioavailable Inhibitor of Factor XIa in Clinical Studies for Antithrombotic Therapy.

Journal of medicinal chemistry·2021

Related Experiment Video

Updated: Jul 13, 2026

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

Loopholes and missing links in protein modeling.

Karen A Rossi1, Carolyn A Weigelt, Akbar Nayeem

  • 1Computer-Assisted Drug Design, Pharmaceutical Research Institute, Bristol-Myers Squibb Company, Princeton, New Jersey 08543, USA. karen.rossi@bms.com

Protein Science : a Publication of the Protein Society
|July 31, 2007
PubMed
Summary

This study compared four loop modeling programs, finding accuracy varied with loop length. Prime performed best for longer loops, but all programs struggled to rank the most accurate models.

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

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

Related Experiment Videos

Last Updated: Jul 13, 2026

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

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

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

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein modeling

Background:

  • Accurate protein loop modeling is crucial for understanding protein structure and function.
  • Several software programs exist for loop sampling, employing diverse methodologies.
  • An unbiased comparison of these tools is needed to guide researchers.

Purpose of the Study:

  • To provide an unbiased comparison of four leading loop modeling programs: Prime, Modeler, ICM, and Sybyl.
  • To assess the quality of modeled loops and identify the strengths and weaknesses of each method.
  • To evaluate program performance across varying loop lengths (4-12 amino acids).

Main Methods:

  • Comparison of four commercially available loop modeling programs.
  • Classification of methods into ab initio generation (Modeler, Prime) and database searches (Sybyl, ICM).
  • Assessment of accuracy by comparing modeled loops to native structures using Root Mean Square Deviation (RMSD).

Main Results:

  • All programs performed similarly for short loops (4-6 residues).
  • Program accuracy diverged for longer loops; Prime achieved RMSD <2.5 Å for loops up to 10 residues.
  • Disulfide bonds and crystal packing influenced results; no program consistently ranked the lowest RMSD model highest.

Conclusions:

  • Loop modeling accuracy is dependent on loop length and the specific software protocol used.
  • Prime demonstrated superior performance for longer loops compared to Modeler, ICM, and Sybyl.
  • Current loop modeling software exhibits limitations in accurately ranking the generated models based on structural similarity to the native state.