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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...

Ligand Binding Sites

Ligand Binding Sites

Protein-Protein Interfaces

Protein-Protein Interfaces

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...

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

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Related Experiment Video

Updated: Nov 6, 2025

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

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

LZerD webserver for pairwise and multiple protein-protein docking.

Charles Christoffer¹, Siyang Chen¹, Vijay Bharadwaj¹

¹Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.

Nucleic Acids Research

|May 8, 2021

Summary

This summary is machine-generated.

Computational protein-protein docking tools predict 3D structures of protein complexes when experimental data is unavailable. The LZerD webserver offers advanced docking tools, LZerD and Multi-LZerD, for accurate modeling of protein interactions.

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

Published on: July 25, 2013

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Last Updated: Nov 6, 2025

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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Published on: July 8, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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

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

Published on: July 25, 2013

Area of Science:

Structural biology
Computational biology
Biochemistry

Background:

Protein complexes are crucial for cellular functions.
Determining the 3D structures of protein complexes is essential for understanding cellular mechanisms.
Experimental structure determination can be challenging, necessitating computational approaches.

Purpose of the Study:

To present a webserver providing access to the LZerD and Multi-LZerD protein docking tools.
To offer a user-friendly platform for computationally modeling protein complex structures.
To enable the incorporation of distance constraints for enhanced docking accuracy.

Main Methods:

Utilizing LZerD for pairwise protein docking and Multi-LZerD for multi-chain docking.
Employing a soft protein surface representation with 3D Zernike descriptors and geometric hashing.
Integrating user-defined distance constraints for residue interactions and interface localization.

Main Results:

The LZerD webserver provides access to robust protein docking tools.
The docking protocol consistently ranked high in CAPRI blind evaluations.
The server outputs full-atom docked models and visualizes binding pose distributions.

Conclusions:

The LZerD webserver is a valuable resource for computational protein-protein docking.
The tools facilitate the modeling of complex protein interactions.
The platform supports structural biology research by providing accurate protein complex models.