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Related Concept Videos

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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...

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Related Experiment Video

Updated: Jul 10, 2026

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

A new seed selection algorithm that maximizes local structural similarity in proteins.

Gulsah Altun, Wei Zhong, Yi Pan

    Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
    |October 20, 2007
    PubMed
    Summary

    We developed a new algorithm to improve protein sequence alignment by enhancing seed quality. This method ensures better identification of local structures for more accurate sequence comparisons.

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

    Published on: July 14, 2015

    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Structural Bioinformatics

    Background:

    • Protein sequence alignment is crucial for understanding protein function and evolution.
    • The PHI-BLAST algorithm relies on identifying high-similarity seeds for accurate alignment.
    • The quality of these seeds directly impacts the overall success of the alignment process.

    Purpose of the Study:

    • To propose a novel algorithm for improving the quality of seeds used in protein sequence alignment.
    • To maximize the likelihood that identified seeds share similar local structures between query and known sequences.

    Main Methods:

    • Developed a new algorithm focused on maximizing the likelihood of shared local structure in seeds.
    • Tested the algorithm on the PISCES database, comprising 2290 protein sequences.

    Main Results:

    • The proposed algorithm provides an effective a priori estimate of seed structural quality.
    • Demonstrated improved seed quality for protein sequence alignment.

    Conclusions:

    • The new algorithm enhances the reliability of seed selection in protein sequence alignment.
    • This advancement contributes to more accurate protein sequence analysis and structural prediction.