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Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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 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...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
MO Theory and Covalent Bonding02:40

MO Theory and Covalent Bonding

The molecular orbital theory describes the distribution of electrons in molecules in a manner similar to the distribution of electrons in atomic orbitals. The region of space in which a valence electron in a molecule is likely to be found is called a molecular orbital. Mathematically, the linear combination of atomic orbitals (LCAO) generates molecular orbitals. Combinations of in-phase atomic orbital wave functions result in regions with a high probability of electron density, while...
The Equilibrium Binding Constant and Binding Strength02:18

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:

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Updated: May 22, 2026

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes
09:28

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Published on: January 10, 2017

Modeling molecular recognition: theory and application.

K Mardis1, R Luo, L David

  • 1a Center for Advanced Research in Biotechnology , 9600 Gudelsky Drive , Rockville , MD , 20850.

Journal of Biomolecular Structure & Dynamics
|May 22, 2012
PubMed
Summary
This summary is machine-generated.

Calculating binding affinities for noncovalent complexes is crucial for drug discovery. Our new method uses predominant states, an empirical force field, and continuum electrostatics for efficient molecular design.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Biophysics

Background:

  • Accurate calculation of binding affinities is essential for advancing drug discovery and separation science.
  • Existing methods often lack the speed or physical detail required for practical molecular design.

Purpose of the Study:

  • To present and review an efficient computational method for calculating binding affinities of noncovalent complexes.
  • To demonstrate the method's applicability across various molecular systems.

Main Methods:

  • Utilizes the predominant states method for free energy computation.
  • Employs an empirical force field for molecular interactions.
  • Incorporates an implicit solvation model based on continuum electrostatics.

Main Results:

  • The described method balances significant physical detail with computational speed.
  • Successfully applied to diverse systems, including small molecules and protein-ligand complexes.

Conclusions:

  • The presented computational approach offers an efficient and reliable tool for molecular design.
  • This method facilitates advancements in drug discovery and separation science through accurate binding affinity predictions.