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Related Concept Videos

Protein Families02:47

Protein Families

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 locations, protein...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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.
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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...
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...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Michael Ryan1, Mark Diekhans, Stephanie Lien

  • 1Department of Bioinformatics, George Mason University, Fairfax, VA, USA.

Bioinformatics (Oxford, England)
|April 17, 2009
PubMed
Summary

LS-SNP/PDB provides genome-wide annotation for human non-synonymous single nucleotide polymorphisms (nsSNPs). This resource maps nsSNPs to Protein Data Bank structures, offering valuable protein graphics for biological insights.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Mapping Dysfunctional Protein-Protein Interactions in Disease
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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Area of Science:

  • Genomics
  • Bioinformatics
  • Structural Biology

Background:

  • The human genome contains numerous non-synonymous single nucleotide polymorphisms (nsSNPs) that alter protein sequences.
  • Understanding the structural and functional impact of nsSNPs is crucial for disease research and drug development.

Purpose of the Study:

  • To introduce LS-SNP/PDB, a novel web resource for comprehensive genome-wide annotation of human nsSNPs.
  • To provide high-quality protein visualizations and biologically relevant annotations for nsSNPs.

Main Methods:

  • Systematic mapping of human nsSNPs onto Protein Data Bank (PDB) structures using an automated, high-throughput pipeline.
  • Integration with molecular visualization software (UCSF Chimera) for rendering protein graphics.
  • Annotation of biologically relevant features associated with nsSNPs.

Main Results:

  • LS-SNP/PDB offers detailed annotations for nsSNPs, linking them to specific protein structures.
  • High-quality protein graphics generated by UCSF Chimera facilitate the visualization of SNP effects.
  • The resource is continuously updated through an automated build pipeline.

Conclusions:

  • LS-SNP/PDB serves as a valuable WWW resource for the annotation of human nsSNPs.
  • It enhances understanding of nsSNP impact through integrated structural and functional data.
  • The system's automated updates ensure the provision of current and relevant information.