Sequence Structure Alignment
Sequence Structure Alignment - Related Videos
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Cited by 2 •
2017
A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.
16:02
Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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Cited by 3 •
2023
Here, we present a protocol to utilize the latest version of the US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool. This protocol demonstrates the application of the online tool to rapidly analyze protein conservation and provide customizable and easily interpretable predictions of chemical susceptibility across species.
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Cited by 3 •
2022
The protocol provides instruction for modifying RNA with dimethyl sulfate for mutational profiling experiments. It includes in vitro and in vivo probing with two alternative library preparation methods.
11:36
Assembly, Loading, and Alignment of an Analytical Ultracentrifuge Sample Cell
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Cited by 21 •
2009
The analytical ultracentrifuge (AUC) sample cell holds sample and reference buffer and during experiments and is exposed to high vacuum and rotor speeds up to 60,000 rpm. This video will demonstrate the rigorous attention to detail necessary for assembly, loading and alignment of this very important component of an AUC experiment.
07:12
Microengineering 3D Collagen Hydrogels with Long-Range Fiber Alignment
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Cited by 3 •
2022
This protocol demonstrates the use of a microfluidic channel with changing geometry along the fluid flow direction to generate extensional strain (stretching) to align fibers in a 3D collagen hydrogel (<250 µm in thickness). The resulting alignment extends across several millimeters and is influenced by the extensional strain rate.
FAQs
Sequence similarity alone may not fully reveal which residues correspond after insertions, deletions, or mutations. Structural information adds residue positions, secondary-structure features, and spatial arrangement, helping distinguish relationships that remain meaningful despite sequence changes. This combined view can expose conserved regions whose importance is reflected in molecular architecture rather than identical residue order alone.
Gaps represent possible insertions or deletions, while substitutions account for altered residues between compared molecules. Including both features allows the alignment to preserve plausible correspondence instead of treating every difference as a complete mismatch. Their placement helps researchers evaluate whether sequence variation is compatible with conserved structural organization and may have changed molecular shape.
Corresponding residues and conserved regions provide evidence for relationships among biological molecules, including homologous genes and shared domains. Comparing their arrangement also shows how mutations may be tolerated, preserved, or associated with changes in molecular shape. These observations connect evolutionary sequence patterns with structural consequences, supporting more informed interpretations of protein diversification.
The comparison requires biological sequence information together with three-dimensional molecular structure information. Researchers examine residue correspondence, positions, secondary structure, and spatial arrangement while allowing for relevant gaps or substitutions. The resulting alignment can then be assessed for conserved regions and structural consistency, providing a basis for comparative analysis rather than relying on sequence order alone.
An alignment can connect an unknown or incompletely characterized molecule with related sequence and structural information. Conserved residues, regions, and domains provide guidance for modeling the unknown structure and for proposing functional relationships. This use is especially valuable when genomic information is available but molecular architecture has not yet been directly characterized.
Structure-based annotation uses aligned sequence and molecular features to assign meaning to genomic or protein data. Correspondence with known residues, conserved regions, homologous genes, or domains can help predict function and organize relationships among molecules. Researchers can also interpret sequence changes in light of their potential effects on three-dimensional shape and molecular behavior.