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Structural Classification of Joints

Structural Classification of Joints

Joints, also known as articulations, are classified based on their structural characteristics, i.e., based on whether the articulating surfaces of the adjacent bones are directly connected by fibrous connective tissue or cartilage, or whether the articulating surfaces contact each other within a fluid-filled joint cavity. These differences serve to divide the joints of the body into three structural classifications.
A fibrous joint is where the adjacent bones are united by fibrous connective...

Functional Classification of Joints

Functional Classification of Joints

Functional Classification of Joints
The functional classification of joints is determined by the amount of mobility between the adjacent bones. Joints are functionally classified as a synarthrosis or immobile joint, an amphiarthrosis or slightly moveable joint, or as a diarthrosis, a freely moveable joint. Fibrous and cartilaginous joints can be functionally classified as either synarthroses or amphiarthroses, whereas all synovial joints are classified as diarthroses.
Synarthrosis
An...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Ligand Binding and Linkage

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...

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Related Experiment Video

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Author Spotlight: 3D Movement Assessment of Maxillary Posterior Teeth in Clear Aligner Treatment

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Published on: February 23, 2024

Comparative performance of structural aligners in functional domain annotation.

Poorya Mirzavand Borujeni¹, Reza Salavati²

¹Institute of Parasitology, McGill University, Canada.

Journal of Structural Biology

|March 5, 2026

Summary

This summary is machine-generated.

Structure-based protein domain annotation using AlphaFold models shows promise, with Reseek excelling in sensitivity. However, sequence-profile methods like HMMER remain superior for family-level annotation, especially when incorporating profile information.

Keywords:

AlphaFold Domain annotation Pfam Structural alignment

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Informatics

Background:

Accurate protein domain annotation is crucial for understanding protein function.
Databases like Pfam use sequence-derived signatures, but structure-based methods offer higher sensitivity for distantly related proteins.
AlphaFold provides accurate protein structure predictions, enabling new structure-based annotation approaches.

Purpose of the Study:

To systematically evaluate structure-based versus sequence-based methods for Pfam domain annotation.
To benchmark structural aligners (Reseek, Foldseek, TM-align) against sequence-based methods (MMseqs, HMMER).
To assess the impact of profile-derived information on structural annotation performance.

Main Methods:

Benchmarking of three structural aligners and two sequence-based methods using all-against-all and split-family searches.
Evaluation of residue-level alignment accuracy against Pfam multiple sequence alignments.
Investigation of profile-informed rescoring for structural hit ranking.

Main Results:

Reseek demonstrated the highest sensitivity in all-against-all searches (AUC=0.85), outperforming other structural and sequence aligners.
HMMER remained superior in split-family evaluation (max F1=0.991), confirming the strength of sequence-profile methods.
Structural aligners provided more accurate residue-level mappings than pairwise sequence methods.
Profile-informed rescoring improved performance for short domains.

Conclusions:

Structure-based methods, particularly Reseek, show high sensitivity for protein domain annotation, especially at low sequence identities.
Sequence-profile methods like HMMER are still optimal for family-level annotation.
Combining structural information with sequence profiles offers a promising direction for enhanced domain annotation.