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Related Concept Videos

Ligand Binding Sites02:40

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 Sites02:40

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...
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...
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...
Noncovalent Attractions in Biomolecules02:35

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,...
Ligand Binding and Linkage00:49

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 the...

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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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A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity.

Wenjia Luo1, Jianfeng Pei, Yushan Zhu

  • 1Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China.

Journal of Molecular Modeling
|October 14, 2009
PubMed
Summary
This summary is machine-generated.

A new fast docking algorithm, H-DOCK, excels at identifying drug candidates by prioritizing hydrogen bonds and shape complementarity. This efficient method achieves high success rates for both rigid and flexible ligand docking, aiding drug discovery.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • High-throughput virtual screening is crucial for drug discovery due to advances in protein structure determination.
  • Efficient algorithms are needed to screen large compound libraries against disease targets.

Purpose of the Study:

  • To develop a fast docking algorithm (H-DOCK) for virtual screening.
  • To evaluate H-DOCK's accuracy and efficiency in protein-ligand docking.

Main Methods:

  • Developed H-DOCK using a divide-and-conquer strategy for hydrogen bond matching and surface shape complementarity.
  • Employed a scoring function based on van der Waals interactions.
  • Tested rigid ligand docking on 271 complexes and flexible ligand docking on 93 complexes.

Main Results:

  • H-DOCK achieved a 91.1% success rate for rigid ligand docking (RMSD<2.0 Å).
  • H-DOCK reached an 81.7% success rate for flexible ligand docking.
  • Docking times averaged 0.14 seconds for rigid and 8.25 seconds for flexible ligands.

Conclusions:

  • H-DOCK effectively utilizes hydrogen bonding and steric hindrance for accurate protein-ligand interaction prediction.
  • The algorithm's speed and accuracy make it suitable for large-scale virtual screening as a pre-filter.