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The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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

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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.
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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.
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Related Experiment Video

Updated: Jul 14, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

The BOS-Lig Data Set: Accurate Ligand Charges from a Consensus Approach for 66,810 Experimentally Synthesized

Roland G St Michel^1,2, Ryan J Jang², Aaron G Garrison³

¹Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.

Journal of Chemical Information and Modeling

|July 13, 2026

Summary

Researchers created the Boston Open-Shell Ligand (BOS-Lig) dataset by assigning net charges to ligands in transition metal complexes. This dataset links ligand charge and function, aiding computational screening and ligand design.

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Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Area of Science:

Computational chemistry
Materials science
Crystallography

Background:

Accurate ligand properties are crucial for computational screening of transition metal complexes.
Crystallographic data often lacks consistent or complete information on ligand net charge and application areas.

Purpose of the Study:

To construct a comprehensive ligand dataset with reliable net charge assignments and functional classifications.
To address the limitations of existing crystallographic data for computational chemistry applications.

Main Methods:

Curated 126,985 mononuclear transition metal complexes from the Cambridge Structural Database.
Developed an iterative charge-balancing workflow combining complex charges, metal oxidation states, and crystallographic data.
Classified ligands by coordinating atoms, hemilability, and linked them to application areas using topic modeling.

Main Results:

Assigned confident net charges to 66,810 ligands from 94,581 unique ligand structures, creating the Boston Open-Shell Ligand (BOS-Lig) dataset.
Successfully inferred charges in complex heteroleptic environments where direct data was unavailable.
Linked 25,146 ligands to functional application areas including reactivity, redox, biological, and photophysical chemistry.

Conclusions:

The BOS-Lig dataset provides an experimentally grounded resource connecting ligand charge, structure, and function.
This dataset serves as a foundation for improved computational screening and data-driven design of ligands for transition metal complexes.