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Protein Organization

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.

Conserved Binding Sites

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...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

Protein Families

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...

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Related Experiment Video

Updated: Jun 21, 2026

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

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

Published on: January 26, 2024

Fast and accurate automatic structure prediction with HHpred.

Andrea Hildebrand¹, Michael Remmert, Andreas Biegert

¹Gene Center and Center for Integrated Protein Science (Munich), Ludwig-Maximilians-University Munich, 81377 Munich, Germany.

|July 24, 2009

Summary

This summary is machine-generated.

Automated protein structure prediction servers like HHpred are advancing biological research. HHpred offers competitive accuracy, usability, and fast response times for protein modeling.

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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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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Published on: May 31, 2013

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Automated protein structure prediction is crucial for biological research.
Improvements in automated servers have enhanced homology modeling capabilities.
Detecting and aligning remote homologous templates is key to accurate modeling.

Purpose of the Study:

To describe the HHpred server's automated versions used in CASP8.
To highlight HHpred's unique combination of features.
To assess HHpred's performance against other leading servers.

Main Methods:

Utilized three fully automated HHpred server versions.
Participated in the CASP8 (Critical Assessment of protein Structure Prediction 8) competition.
Focused on homology modeling by detecting and aligning remote templates.

Main Results:

HHpred demonstrated competitive model accuracy in CASP8.
The server offered a unique combination of usability and speed.
Response times were typically under 15 minutes.

Conclusions:

HHpred is a viable and competitive tool for automated protein structure prediction.
The server's performance supports its mainstream adoption in biological research.
HHpred's efficiency and accuracy make it valuable for researchers.