Related Experiment Video
Updated: May 14, 2026
05:08
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
Mining tertiary structural motifs for assessment of designability
1Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA.
Methods in Enzymology
|February 21, 2013
Summary
Scientists developed MaDCaT, a new method to assess protein tertiary structural motif designability. This tool analyzes sequence preferences, aiding in protein design and structure prediction.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Limited secondary-structural alphabets and sequence preferences in proteins have guided protein design and structure prediction.
- The growth of structural genomics data enables extending these analyses to tertiary structural motifs.
Purpose of the Study:
- To introduce a method for assessing the designability of tertiary structural motifs.
- To establish structure/sequence links for encoding designable motifs.
Main Methods:
- Developed MaDCaT, a structural similarity search methodology.
- MaDCaT identifies detailed geometric matches, unlike methods focusing on global topology.
- Assessed designability landscapes of two tertiary structural motifs using MaDCaT.
Main Results:
- Demonstrated the utility of MaDCaT in evaluating tertiary motif designability.
- Established structure/sequence links by identifying necessary sequence constraints for designable motifs.
Conclusions:
- Tertiary structural preferences, analogous to secondary-structure preferences, are valuable for de novo protein design.
- The MaDCaT method facilitates understanding and predicting protein structures based on tertiary motifs.
More Related Videos
Related Concept Videos
01:22Protein Folding
Overview
01:22Design Consideration
Designing a structure involves a series of considerations, primarily the material's ultimate strength, calculated through tests that measure changes under increased force until the material reaches its breaking point or limit. The ultimate load, where the material breaks, is divided by its original cross-sectional area, resulting in the ultimate normal stress or strength. The ultimate shearing stress is another significant factor taken into account.
The factor of safety is another key aspect...
The factor of safety is another key aspect...
01:25Yield Criteria for Ductile Materials under Plane Stress
In designing structural elements and machine parts using ductile materials, it is crucial to ensure that these components withstand applied stresses without yielding. Yielding is initially determined through a tensile test, which evaluates the material's response to uniaxial stress. However, tensile stress is insufficient when components face biaxial or plane stress conditions This condition requires advanced criteria to predict failure.
The Maximum Shearing Stress Criterion, also known as the...
The Maximum Shearing Stress Criterion, also known as the...
01:49Conserved 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...
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...
02:15Protein 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...
A protein's shape is critical to its function. For example, an enzyme can...
01:18Indeterminate Structure
Indeterminate structures refer to structures where internal forces and reactions cannot be determined using only the equations of static equilibrium. Indeterminate structures have more unknown forces and reaction forces than equations of static equilibrium that can be used to determine them. Indeterminate structures are often used in engineering to create complex, efficient, and aesthetically pleasing structures. There are various types of indeterminate structures used in engineering and some...