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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...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jun 5, 2026

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project
07:22

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project

Published on: February 11, 2019

Accurate protein stability prediction for small domains using mega-scale experiments.

Yehlin Cho1, Kotaro Tsuboyama2,3, Theodore J Litberg2

  • 1Massachusetts Institute of Technology; Cambridge, MA, USA.

Biorxiv : the Preprint Server for Biology
|June 4, 2026
PubMed
Summary

Researchers developed new models to predict protein folding stability for small protein domains using a large dataset. This breakthrough aids protein design and understanding genetic variations.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Last Updated: Jun 5, 2026

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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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:

  • Biophysics
  • Computational Biology
  • Molecular Biology

Background:

  • Predicting protein folding stability is crucial for protein design and understanding genetic variation.
  • Existing physics-based and machine learning methods have limitations due to computational cost and data scarcity.

Purpose of the Study:

  • To develop accurate predictive models for absolute protein folding stability.
  • To leverage megascale biophysical measurements for enhanced stability prediction.

Main Methods:

  • Utilized cDNA display proteolysis to measure folding stability for 1.8 million protein domains.
  • Developed predictive models SaProtΔG and ESM3ΔG using the "MGnify Stability dataset".

Main Results:

  • Achieved high accuracy in predicting absolute folding stability (RMSE of 0.8 kcal/mol, Spearman correlation of 0.88).
  • Demonstrated accurate prediction of stability changes from mutations (substitutions, insertions, deletions).
  • Identified trends of increased stability in thermophilic organisms and improved discrimination of designed proteins.

Conclusions:

  • Megascale biophysical measurements combined with evolutionary and structural data enable accurate absolute stability prediction for small protein domains.
  • The developed models SaProtΔG and ESM3ΔG represent a significant advancement in predicting protein folding stability.