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Protein-protein Interfaces

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...

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...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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.

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Related Experiment Video

Updated: Jun 18, 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

Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical

Laura Pérez-Cano¹, Albert Solernou, Carles Pons

¹Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona 29, Barcelona 08034, Spain.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

|November 13, 2009

Summary

This study introduces a new computational method for protein-RNA docking, using statistical potentials to score potential complexes. The approach successfully improves the accuracy of predicting near-native protein-RNA structures.

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Last Updated: Jun 18, 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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Protein Target Prediction and Validation of Small Molecule Compound

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Area of Science:

Structural biology
Computational biology
Biochemistry

Background:

Protein-RNA interactions are crucial in cells, but structural data is limited.
Few computational methods exist for protein-RNA complex prediction, lacking systematic benchmarking.

Purpose of the Study:

To develop and benchmark a novel computational approach for protein-RNA docking.
To introduce new statistical potentials for scoring protein-RNA docking poses.

Main Methods:

Extracted pairwise residue-ribonucleotide interface propensities.
Developed a protein-RNA docking protocol using FTDock for pose generation and propensity-based scoring.
Benchmarked the method on 12 protein-RNA complex cases.

Main Results:

FTDock generated near-native solutions in over 50% of cases.
Propensity-based scoring improved docking results, ranking near-native solutions within the top 100 in 43% of cases.
The method demonstrated effective scoring for selecting promising docking orientations.

Conclusions:

The developed protein-RNA docking protocol is effective and improves prediction accuracy.
Statistical residue-ribonucleotide potentials offer a valuable scoring mechanism for protein-RNA docking.
This method facilitates the selection of candidate poses for further refinement.