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Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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.
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.
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

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Related Experiment Video

Updated: May 16, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Reading PDB: perception of molecules from 3D atomic coordinates.

Sascha Urbaczek1, Adrian Kolodzik, Inken Groth

  • 1Center for Bioinformatics (ZBH), University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

Journal of Chemical Information and Modeling
|November 27, 2012
PubMed
Summary

This study introduces a new method for generating valid molecular structures from atomic coordinates, achieving a 98% success rate even with low-quality data. This approach enhances cheminformatics and drug development by reliably processing structural data.

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Related Experiment Videos

Last Updated: May 16, 2026

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Area of Science:

  • Cheminformatics
  • Structural Biology
  • Computational Chemistry

Background:

  • Small molecule crystal structure analysis is crucial for drug development.
  • Structural data from atomic coordinates lacks inherent chemical validity.
  • Existing methods struggle with experimental uncertainties and low-resolution data.

Purpose of the Study:

  • To develop a robust method for generating chemically valid molecular structures from atomic coordinates.
  • To improve the reliability of molecular structure perception from potentially distorted experimental data.
  • To provide a dependable basis for subsequent computational analyses in drug discovery.

Main Methods:

  • Utilized the recently published NAOMI model for a consistent chemical description.
  • Developed a novel method for molecular structure generation from 3D atomic coordinates.
  • Assessed robustness by processing all small molecules from the Protein Data Bank (PDB).

Main Results:

  • Achieved a 98% success rate in perceiving molecules from 363 PDB entries.
  • Demonstrated reliable results even with low-quality input data, outperforming previous methods.
  • Processed the complete PDB small molecule dataset in under 3 minutes, proving scalability.

Conclusions:

  • The presented method reliably generates chemically valid molecular structures from atomic coordinates.
  • The approach is robust against experimental uncertainties and data quality variations.
  • The method's efficiency and accuracy make it suitable for large-scale cheminformatics applications and drug development.