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Related Concept Videos

Carbon Skeletons01:12

Carbon Skeletons

Life on Earth is carbon-based, as all macromolecules that make up living organisms contain carbon atoms. All organic compounds have a carbon backbone. Each carbon atom is tetravalent and can bond with four other atoms, making it an extraordinarily flexible component of biological molecules. Because carbon’s valence electrons are stable, it rarely becomes an ion. As the carbon chain increases in length, structural modifications such as ring structures, double bonds, and branching side chains...
Structure of Alkanes02:23

Structure of Alkanes

The formation of carbon-carbon bonds leading to the creation of the carbon chain is the basis of organic chemistry. August Kekulé and Archibald Scott Couper independently developed this idea of carbon chain formation.
Hydrocarbons are the simplest organic compounds composed of carbons and hydrogens. Based on the bond order between carbons, the hydrocarbons are further classified into alkanes, alkenes, and alkynes. 
Alkanes are the simplest hydrocarbons with sp3 hybrid carbon atoms. These sp3...
Structures of Carboxylic Acid Derivatives01:28

Structures of Carboxylic Acid Derivatives

Structure of Carboxylic Acid Derivatives
Carboxylic acid derivatives contain an acyl group attached to a heteroatom such as chlorine, oxygen, or nitrogen. The carbonyl carbon and oxygen are both sp2-hybridized with an unhybridized p orbital.
The three sp2 orbitals of the carbonyl carbon form three σ bonds, one each with the carbonyl oxygen, the α carbon, and the heteroatom, whereas the other two sp2 orbitals of the carbonyl oxygen are occupied by the lone pairs. Further, the unhybridized p...
Structures of Aldehydes and Ketones01:04

Structures of Aldehydes and Ketones

Vanillin—a flavoring agent in vanilla, cinnamaldehyde—a molecule responsible for the distinct smell of cinnamon, and acetone—a strong-smelling ingredient in nail polish removers, all belong to a class of carbonyl compounds called aldehydes and ketones (Figure 1). Although both aldehydes and ketones contain the characteristic carbonyl (C=O) bond, their chemical structures vary with respect to the groups directly attached to the carbonyl carbon.
In aldehydes (Figures 1a and 1b), the carbonyl...
¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
Amino acids03:42

Amino acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...

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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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Pocket similarity: are alpha carbons enough?

Howard J Feldman1, Paul Labute

  • 1Chemical Computing Group, Inc., 1010 Sherbrooke Street West, Suite 910, Montreal, Quebec, Canada H3A 2R7. hfeldman@chemcomp.com

Journal of Chemical Information and Modeling
|August 10, 2010
PubMed
Summary

A new method uses alpha carbon positions to measure protein pocket similarity, enabling effective clustering and identification of related protein families and kinase subfamilies.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein binding sites are crucial for function and drug discovery.
  • Accurate comparison of protein pockets is essential for understanding protein families and designing targeted therapies.
  • Existing methods may be computationally intensive or lack sufficient accuracy.

Purpose of the Study:

  • To develop a novel, efficient, and accurate method for assessing protein pocket similarity.
  • To utilize this method for clustering diverse protein families and kinase subfamilies based solely on binding site information.
  • To establish the sensitivity and specificity of the developed method for practical applications.

Main Methods:

  • A novel protein pocket similarity measurement was devised using only alpha carbon (Calpha) positions of pocket residues.

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  • Pairwise pocket comparison employed an exhaustive 3D Calpha common subset search, with residue grouping by physicochemical properties.
  • An Extreme Value Distribution fit to distances between Calpha matches generated a probabilistic similarity score.

    • Main Results:

    • Clustering of 85 structures from 13 protein families based on binding sites alone was successfully achieved.
    • 25 kinases were accurately clustered into subfamilies using the developed scoring system.
    • A test kinase query demonstrated high specificity (99.2%) and sensitivity (97.5%) with an appropriate score cutoff.
    • The entire Protein Data Bank (133,800 pockets) was searchable within 2-10 minutes on a single CPU.

    Conclusions:

    • The novel Calpha-based method provides an efficient and accurate approach for protein pocket similarity measurement.
    • This method is effective for unsupervised clustering of proteins and identification of functional relationships based on binding sites.
    • The high specificity and sensitivity indicate its potential for large-scale database searching and drug discovery applications.