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

8.9K
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....
8.9K
Protein Families02:47

Protein Families

16.6K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
16.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
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...
14.4K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

46.6K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
46.6K
Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
5.0K
Protein and Protein Structure02:15

Protein and Protein Structure

86.3K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
86.3K

You might also read

Related Articles

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

Sort by
Same author

Photochemical reductive coupling of α-keto esters for synthesizing 2,3-diarylated tartaric acid esters.

Organic & biomolecular chemistry·2026
Same author

ZDHHC18-Mediated Palmitoylation of ORF3a Promotes SARS-CoV-2 Pathogenesis by Antagonizing TRIM16-Mediated Ubiquitination and Proteasomal Degradation.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Cross-chemical and cross-species toxicity prediction: benchmarking and a novel 3D-structure-based deep learning model.

Environmental toxicology and chemistry·2026
Same author

Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.

Microbiology spectrum·2026
Same author

A Single Concussion in Juvenile Mice Leads to Sex Specific Acute Cerebral Vascular Dysfunction and Blood-brain Border Dysfunction.

Research square·2026
Same author

FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra.

Nature communications·2025
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

Related Experiment Video

Updated: Jan 2, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K

Database searching by flexible protein structure alignment.

Yuzhen Ye1, Adam Godzik

  • 1Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. yye@burnham.org

Protein Science : a Publication of the Protein Society
|June 25, 2004
PubMed
Summary
This summary is machine-generated.

Flexible protein structure alignment (FATCAT) now includes statistical significance estimation, enabling its use in database searching for functional annotations. This method is comparable to rigid-body programs and reveals conformational flexibilities potentially linked to function or evolution.

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.9K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Related Experiment Videos

Last Updated: Jan 2, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.4K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.9K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.6K

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure alignment is crucial for functional annotation.
  • Existing flexible alignment methods lack statistical significance estimation for database searching.
  • FATCAT (Flexible Alignment Tool for Computational Analysis of Structures) was developed to address protein flexibility.

Purpose of the Study:

  • To develop a statistical significance estimation for FATCAT alignment scores.
  • To enable FATCAT as a database-searching tool for identifying similar protein structures.
  • To evaluate the impact of flexibility on structure comparison sensitivity and specificity.

Main Methods:

  • Developed a statistical significance estimation for FATCAT alignment scores.
  • Analyzed the distribution of FATCAT similarity scores for unrelated protein structures.
  • Compared FATCAT's performance against rigid-body structure comparison programs (DALI, CE).

Main Results:

  • FATCAT alignment scores for unrelated proteins follow an extreme value distribution (EVD).
  • Incorporating flexibility minimally affects the sensitivity and specificity of structure identification.
  • FATCAT demonstrates comparable performance to DALI and CE in database searching.
  • Identified conformational flexibilities potentially related to substrate specificity and structural evolution.

Conclusions:

  • The statistical significance estimation allows FATCAT to be effectively used as a database searching tool.
  • Flexible structure alignment provides valuable insights into protein function and evolution.
  • FATCAT offers a powerful alternative for large-scale structural database analysis.