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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...
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...
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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Non-equilibrium in the Cell01:16

Non-equilibrium in the Cell

An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction. The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system...
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...

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Updated: Jul 5, 2026

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

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Published on: July 25, 2013

Generative AI for controllable protein sequence design: A survey.

Yiheng Zhu1, Zitai Kong2, Jialu Wu3

  • 1Zhongguancun Academy, Beijing, China.

Npj Drug Discovery
|July 3, 2026
PubMed
Summary
This summary is machine-generated.

Generative artificial intelligence (AI) is revolutionizing protein engineering by enabling the design of novel protein sequences with specific functions. This survey reviews AI advancements for controllable protein design, addressing challenges in the field.

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

Published on: January 26, 2024

Area of Science:

  • Protein Engineering
  • Artificial Intelligence
  • Computational Biology

Background:

  • Designing novel protein sequences with desired functions is crucial for drug discovery and enzyme engineering.
  • The vast search space of protein sequences presents significant time and financial challenges.
  • Advancements in artificial intelligence (AI) are transforming protein design capabilities.

Purpose of the Study:

  • To systematically review recent progress in generative AI for controllable protein sequence design.
  • To outline foundational protein design tasks, constraints, and key AI models.
  • To identify current challenges and future research opportunities in the field.

Main Methods:

  • Review of generative AI models and optimization algorithms for protein sequence design.
  • Analysis of different protein design tasks and their associated constraints.
  • Discussion of in silico evaluation methods and practical applications.

Main Results:

  • Generative AI models offer powerful tools for navigating the complex protein sequence space.
  • The survey covers foundational concepts, advanced models, and evaluation strategies.
  • Key applications in drug discovery and enzymatic engineering are highlighted.

Conclusions:

  • Generative AI represents a new era in controllable protein sequence design.
  • Addressing current challenges will further unlock AI's potential in protein engineering.
  • Future research should focus on expanding AI applications and improving design methodologies.