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Related Concept Videos

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...
What are Proteins?01:55

What are Proteins?

Overview
Basicity of Aliphatic Amines01:21

Basicity of Aliphatic Amines

Amines can behave as Brønsted–Lowry bases by accepting a proton from the acid to form corresponding conjugate acids. Due to a lone pair of nonbonding electrons, aliphatic amines can also act as Lewis bases by forming a covalent bond with an electrophile.
To measure the basicity of amines, two conventions are generally used. The first defines Kb as the basicity constant for the deprotonation reaction of water by the amine, as presented in Figure 1. Conventionally, lower Kb indicates higher...
Physical Properties of Amines01:26

Physical Properties of Amines

Amines with low molecular weight are usually gaseous at room temperature, while those with high molecular weight are liquid or solids in nature. Usually, low molecular weight amines have a rotten fish-like smell. Diamines typically have a pungent smell. For instance, cadaverine and putrescine, depicted in Figure 1, are two molecules responsible for decaying tissue.
Basicity of Heterocyclic Aromatic Amines01:25

Basicity of Heterocyclic Aromatic Amines

Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).
What are Proteins?01:28

What are Proteins?

Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight.  Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional structure...

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Related Experiment Video

Updated: Jul 14, 2026

Determination of the Gas-phase Acidities of Oligopeptides
11:00

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

APDbase: Amino acid Physico-chemical properties Database.

Venkatarajan S Mathura1, Deepak Kolippakkam

  • 1Roskamp Institute, 2040 Whitfield Avenue, Sarasota, FL 34243, USA. venkatms11@gmail.com

Bioinformation
|June 29, 2007
PubMed
Summary

This study details APDbase, a new database of 242 physico-chemical properties for all 20 amino acids. It aids in studying protein sequences, folding, and function, offering query and data deposition features.

Area of Science:

  • Biochemistry
  • Bioinformatics

Background:

  • Physico-chemical properties of amino acids are crucial for understanding protein characteristics.
  • Existing data on these properties are fragmented, hindering comprehensive analysis.

Purpose of the Study:

  • To create a centralized, comprehensive database of amino acid physico-chemical properties.
  • To facilitate research into protein sequence profiles, folding, and function.

Main Methods:

  • Collated 242 physico-chemical properties for the 20 naturally occurring amino acids.
  • Developed a searchable database named APDbase (Amino acid Physico-chemical properties Data base).

Main Results:

  • APDbase provides a unified resource for 242 amino acid properties.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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  • The database allows querying by property keywords or index numbers.
  • Includes references for all property values and supports new data deposition.

    • Conclusions:

    • APDbase serves as a valuable, accessible resource for researchers in biochemistry and bioinformatics.
    • The database structure supports ongoing data enrichment and user contributions.