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Related Concept Videos

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Prodepth: predict residue depth by support vector regression approach from protein sequences only.

Jiangning Song1, Hao Tan, Khalid Mahmood

  • 1Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia. Jiangning.Song@med.monash.edu.au

Plos One
|September 18, 2009
PubMed
Summary

Residue depth (RD), a measure of protein burial, can now be accurately predicted from amino acid sequences. This advance in structural bioinformatics aids in identifying key functional residues using computational methods.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Science

Background:

  • Residue depth (RD) quantifies residue burial within protein structures, complementing accessible surface area (ASA).
  • RD correlates with protein stability, conservation, and amino acid type, indicating its biological significance.
  • Accurate RD prediction from sequence is crucial for identifying functionally important residues, folding nuclei, and active sites.

Purpose of the Study:

  • To develop an efficient computational approach for predicting residue depth (RD) solely from protein sequences.
  • To investigate the impact of various sequence encoding schemes on RD prediction accuracy.
  • To evaluate the performance of support vector regression for quantifying the RD-sequence relationship.

Main Methods:

  • Employed support vector regression (SVR) to model the relationship between protein sequence and residue depth.
  • Systematically evaluated eight sequence encoding schemes, encompassing both local and global sequence characteristics.
  • Utilized 5-fold cross-validation to objectively assess prediction accuracy, reporting correlation coefficient (CC) and root mean square error (RMSE).

Main Results:

  • Achieved a correlation coefficient (CC) of 0.71 and a root mean square error (RMSE) of 1.74 between observed and predicted RD values.
  • Demonstrated that residue depth can be reliably predicted using only protein primary sequences.
  • Identified local sequence environments as the primary determinants of RD, with global features having a marginal influence.

Conclusions:

  • The developed SVR approach provides a reliable method for predicting residue depth from protein sequences.
  • This capability has significant implications for structural bioinformatics, protein structure prediction, and homology modeling.
  • The method offers a powerful new tool for sequence analysis and understanding protein structure-function relationships.