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Related Concept Videos

Atomic Orbitals02:44

Atomic Orbitals

An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.
Hybridization of Atomic Orbitals II03:35

Hybridization of Atomic Orbitals II

sp3d and sp3d 2 Hybridization
Hybridization of Atomic Orbitals I03:24

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Updated: Jun 8, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

PZIM: a method for similarity searching using atom environments and 2D alignment.

Anders E Berglund1, Richard D Head

  • 1Exploratory Immunobiology Inflammation & Immunology Research Unit, Pfizer Global Research and Development, Chesterfield, Missouri 63017, United States. anders.e.berglund@pfizer.com

Journal of Chemical Information and Modeling
|October 5, 2010
PubMed
Summary

A new method called PZIM enhances small molecule database searches by analyzing atom environments. This approach offers flexible similarity definitions and outperforms existing methods in identifying molecules with desired properties.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Searching large small molecule databases for specific properties is challenging.
  • Existing similarity searching algorithms have varied strengths and weaknesses due to the ambiguous definition of "similarity".

Purpose of the Study:

  • To introduce PZIM, a novel similarity searching approach for small molecule databases.
  • To enable tailored similarity searches based on user-defined criteria.

Main Methods:

  • PZIM utilizes a description of the atom environment with adjustable features.
  • It incorporates an atom-substitution matrix for identifying similar pharmacophoric elements.
  • The method generates 2D molecular alignments for molecules exceeding a similarity threshold.

Main Results:

  • PZIM was compared against seven other similarity searching methods across nine datasets.
  • It achieved a first or second rank in most test cases.
  • PZIM obtained the highest average rank score among all tested methods.

Conclusions:

  • PZIM demonstrates significant effectiveness in similarity searching across various conditions.
  • The approach offers a flexible and powerful tool for exploring chemical databases.
  • Its performance highlights the advantages of its atom environment-based strategy.