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Related Concept Videos

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...
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...
VSEPR Theory02:37

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
VSEPR Theory and the Basic Shapes02:52

VSEPR Theory and the Basic Shapes

Overview of VSEPR Theory

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Related Experiment Video

Updated: May 29, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Rapid shape-based ligand alignment and virtual screening method based on atom/feature-pair similarities and volume

G Madhavi Sastry1, Steven L Dixon, Woody Sherman

  • 1Schrödinger, Sanali Infopark, 8-2-120/113 Banjara Hills, Hyderabad 500034, Andhra Pradesh, India.

Journal of Chemical Information and Modeling
|August 30, 2011
PubMed
Summary

Phase Shape is a novel computational method for drug design. It rapidly aligns molecules and efficiently identifies active compounds in virtual screening, improving drug discovery accuracy.

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Related Experiment Videos

Last Updated: May 29, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Area of Science:

  • Computational chemistry
  • cheminformatics
  • drug discovery

Background:

  • Shape-based methods are crucial for computer-aided drug design (CADD).
  • Accurate ligand alignment and scoring are essential for virtual screening success.

Purpose of the Study:

  • To introduce Phase Shape, a new flexible ligand superposition and virtual screening method.
  • To demonstrate Phase Shape's ability to rapidly produce accurate 3D alignments and enrich active compounds.

Main Methods:

  • Utilizes atom distribution triplets for rapid trial alignments.
  • Refines alignments to maximize volume overlap.
  • Offers shape-only, atom-type, and pharmacophore feature encoding options.

Main Results:

  • Phase Shape consistently produces accurate 3D ligand alignments, validated against crystal structures.
  • The method effectively enriches active compounds in virtual screening across eleven diverse targets.
  • Performance is comparable or superior to existing shape-based methods.

Conclusions:

  • Phase Shape is an efficient and accurate tool for flexible ligand alignment and virtual screening.
  • Pharmacophore feature encoding enhances database screening performance.
  • The method offers a valuable addition to the computer-aided drug design toolkit.