Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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

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 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 the...

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 the...

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...

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Modeling the Sensitivity of Large-Scale Virtual Screening to Scoring Function Accuracy, Artifacts, and Library Composition.

Journal of chemical information and modeling·2026

Same author

Library Docking for Cannabinoid-2 Receptor Ligands.

Journal of medicinal chemistry·2026

Same author

In-depth multimodal validation of <sup>18</sup>F-THK5351 for imaging monoamine oxidase-B-mediated reactive astrogliosis in Alzheimer's and related neurodegenerative diseases.

Experimental & molecular medicine·2026

Same author

Toward a Random Background for Ligand Optimization.

bioRxiv : the preprint server for biology·2026

Same author

The Selectivity Implications of Docking Libraries with Greater and Lesser Similarities to Bio-like Molecules.

Journal of medicinal chemistry·2026

Same author

Drug-Induced Phospholipidosis as an Artifact in Antiviral Drug Repurposing.

ACS omega·2026

Search research articles

Related Experiment Video

Updated: Jun 9, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Rapid context-dependent ligand desolvation in molecular docking.

Michael M Mysinger¹, Brian K Shoichet

¹Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA.

Journal of Chemical Information and Modeling

|August 26, 2010

Summary

A new context-dependent ligand desolvation scoring term improves molecular docking by accurately accounting for solvent interactions. This method enhances ligand enrichment and docking performance across diverse receptor types with minimal computational cost.

More Related Videos

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Related Experiment Videos

Last Updated: Jun 9, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Area of Science:

Computational chemistry
Drug discovery
Structural biology

Background:

Molecular docking requires accurate scoring of ligand-receptor and ligand-solvent interactions.
Existing desolvation models in docking can be inaccurate for different receptor types.

Purpose of the Study:

To develop and test a context-dependent ligand desolvation scoring term for molecular docking.
To improve the accuracy and reliability of molecular docking algorithms.

Main Methods:

Relating Generalized-Born effective Born radii to fractional desolvation.
Scaling atom-by-atom transfer free energy using fractional desolvation.
Precomputing fractional desolvation on a scoring grid.
Testing performance on 40 DUD targets using property-matched decoys.

Main Results:

Context-dependent desolvation shows improved ligand enrichment compared to raw free energy or ignoring desolvation.
The method enhances docking performance across various receptor types (charged and neutral).
It reliably discriminates ligands from highly charged molecules, outperforming methods that ignore desolvation.

Conclusions:

Context-dependent ligand desolvation offers a physically accurate and computationally efficient scoring approach.
The method is readily incorporable into existing physics-based docking programs.
It enhances docking reliability with minimal impact on calculation time.