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Related Concept Videos

Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
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...
Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Related Experiment Video

Updated: May 31, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Predicting protein folds with fold-specific PSSM libraries.

Yoojin Hong1, Sree Vamsee Chintapalli, Kyung Dae Ko

  • 1Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

Plos One
|June 24, 2011
PubMed
Summary

This study introduces Fold-specific Position Specific Scoring Matrix Libraries (FSL) for protein fold recognition. FSL accurately predicts protein structures from amino acid sequences, even for highly divergent proteins.

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Last Updated: May 31, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

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

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Accurate protein fold assignment is crucial for structural studies but challenging for divergent sequences.
  • Existing methods struggle with identifying distant evolutionary relationships.

Purpose of the Study:

  • To develop an effective method for protein fold recognition using sequence data.
  • To enable accurate prediction of protein structures for highly divergent sequences.

Main Methods:

  • Utilized sets of Position Specific Scoring Matrices (PSSMs), each tailored to a specific protein fold.
  • Developed Fold-specific Position Specific Scoring Matrix Libraries (FSL) for fold recognition.
  • Employed low-identity sequence alignments generated by FSL to detect distant relationships.

Main Results:

  • FSL successfully predicted/related structures from amino acid sequences of highly divergent proteins.
  • The method demonstrated strong performance on the "twilight-zone" SABmark dataset.
  • FSL accurately predicted folds in newly determined protein structures.

Conclusions:

  • FSL offers a reliable method for protein fold recognition, particularly for challenging "twilight-zone" cases.
  • A comprehensive PSSM library for all unique Protein Database (PDB) folds could enable proteomic-level annotation.
  • The FSL method and associated resources are publicly available for broader application.