Related Experiment Video
Updated: May 9, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
CONFECT: conformations from an expert collection of torsion patterns
Christin Schärfer1, Tanja Schulz-Gasch, Jérôme Hert
1Center for Bioinformatics, University of Hamburg, Bundesstraße 46, 20146 Hamburg (Germany).
Chemmedchem
|August 10, 2013
Summary
We developed CONFECT, a new conformation generator for drug design. It efficiently creates smaller, high-quality molecular conformation ensembles using torsion patterns and the Cambridge Structural Database, covering conformational space effectively.
Area of Science:
- Computational chemistry
- Molecular modeling
- Drug discovery
Background:
- Generating low-energy molecular conformations is crucial for drug design.
- Existing methods may produce large or incomplete conformational ensembles.
Purpose of the Study:
- Introduce CONFECT, a novel conformation generator.
- Enable efficient and accurate generation of molecular conformation ensembles.
Main Methods:
- Utilizes a library of torsion patterns.
- Employs normalized frequency distributions from the Cambridge Structural Database (CSD).
- Employs an incremental construction approach with systematic enumeration within energetic boundaries.
Main Results:
- CONFECT efficiently generates high-quality conformation ensembles.
- Ensembles produced by CONFECT are smaller than those from state-of-the-art tools.
- CONFECT effectively covers the conformational space.
Conclusions:
- CONFECT offers an efficient and effective solution for generating molecular conformations in drug design.
- The tool provides smaller yet comprehensive conformational ensembles.
- CONFECT represents an advancement in computational drug design tools.
Related Concept Videos
02:11Conformations of Cyclohexane
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
02:02Chair Conformation of Cyclohexane
The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
02:18Conformations of Ethane and Propane
In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, the...
Staggered conformation is a low energy and more stable conformation with the C-H bonds on the front carbon placed at 60°dihedral angles relative to the C-H bonds on the back carbon, leading to a reduced torsional strain. In staggered ethane, the...
02:29Conformations of Cycloalkanes
Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3 hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that was based on the...
01:16Torsion of Noncircular Members
Circular shafts undergoing torsional stress maintain their cross-sectional integrity due to their axisymmetric nature. This symmetry ensures an even distribution of stress, allowing the shaft to withstand torsion without distorting. In contrast, square bars, lacking this axial symmetry, experience significant distortion across their cross-sections when subjected to torsion, with the exception of along their diagonals and at lines connecting midpoints. A detailed examination of a cubic element...
00:52¹H 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...