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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
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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...

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

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Published on: July 16, 2017

TOPSAN: a dynamic web database for structural genomics.

Kyle Ellrott1, Christian M Zmasek, Dana Weekes

  • 1Joint Center for Structural Genomics, Bioinformatics Core, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

Nucleic Acids Research
|October 22, 2010
PubMed
Summary
This summary is machine-generated.

The Open Protein Structure Annotation Network (TOPSAN) is a web platform aiding researchers in exploring and annotating protein structures. It uses automated information and semantic web technologies to integrate data and facilitate collaborative analysis.

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Last Updated: Jun 7, 2026

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Published on: August 15, 2019

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Structural genomics efforts generate numerous protein structures requiring characterization.
  • Many proteins determined by structural genomics remain uncharacterized, posing a challenge for researchers.
  • A need exists for collaborative platforms to facilitate the annotation and exploration of these protein structures.

Purpose of the Study:

  • To introduce the Open Protein Structure Annotation Network (TOPSAN) as a collaborative platform.
  • To address the challenge of characterizing uncharacterized protein structures.
  • To leverage semantic web technologies for data integration and mining.

Main Methods:

  • Development of a web-based collaboration platform (TOPSAN).
  • Implementation of a user-friendly interface with automatically generated information.
  • Integration of semantic web technologies for linking to external databases.

Main Results:

  • TOPSAN provides a centralized platform for exploring and annotating protein structures.
  • Automated information and semantic web links enrich the platform's content.
  • The platform enables data integration from disparate sources and facilitates data mining.

Conclusions:

  • TOPSAN offers a valuable resource for the structural biology community.
  • The platform enhances collaborative annotation and investigation of protein structures.
  • Semantic web technologies are effective for integrating and analyzing large biological datasets.