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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: May 22, 2026

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

Published on: January 26, 2024

An energy-based conformer library for side chain optimization: improved prediction and adjustable sampling.

Sabareesh Subramaniam1, Alessandro Senes

  • 1Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Proteins
|May 12, 2012
PubMed
Summary
This summary is machine-generated.

We developed an Energy-Based library for protein side chain optimization, improving sampling with an energetic criterion. This method enhances protein structure prediction and design by providing versatile, energetically favorable side chain conformations.

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Last Updated: May 22, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Side chain optimization is crucial for protein modeling tasks like docking and structural prediction.
  • Current methods rely on rotamer or conformer libraries, which may not fully capture energetic preferences.

Purpose of the Study:

  • To improve side chain sampling in protein modeling by introducing an energetic criterion during library creation.
  • To develop an Energy-Based library (EBL) that selects conformations based on their fit within natural protein environments.

Main Methods:

  • Created a conformer library incorporating an energetic criterion for selecting side chain conformations.
  • Developed an ordered list structure for the library, allowing adjustable size and sampling levels.
  • Produced a rotameric version of the library for dihedral-only conformation descriptions.

Main Results:

  • The Energy-Based library significantly improved side chain optimization, yielding lower energy structures.
  • Enhanced prediction accuracy for side chain conformations was achieved.
  • The library's adjustable size offers versatile tuning for sampling in various protein optimization problems.

Conclusions:

  • The Energy-Based library represents a substantial advancement in protein side chain optimization.
  • Its energetic selection and tunable sampling provide greater accuracy and flexibility for protein modeling applications.
  • The libraries are publicly available for use in structural prediction, docking, and protein design.