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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...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence 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...
Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...

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Related Experiment Video

Updated: Jul 17, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Automated site-directed drug design using molecular lattices.

R A Lewis1, D C Roe, C Huang

  • 1Dept. of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446.

Journal of Molecular Graphics
|June 1, 1992
PubMed
Summary

This study introduces BUILDER, a new program for receptor-based drug design. It generates diverse molecular structures complementary to target receptor sites, aiding in the discovery of novel drug candidates.

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

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Receptor-based drug design relies on understanding receptor structure and molecular recognition principles.
  • Drug-receptor interactions are often governed by specific key receptor groups.
  • A common challenge is assembling molecular fragments into structures that fit receptor binding sites.

Purpose of the Study:

  • To present a novel computational program, BUILDER, for generating diverse molecular structures.
  • To demonstrate a new approach for fragment-based drug design within an interactive modeling environment.
  • To showcase the program's utility in designing molecules for specific targets like HIV-1 protease.

Main Methods:

  • Utilizing database searching techniques and structure generation algorithms.
  • Integrating these methods within an interactive graphics modeling environment (MidasPlus).
  • Introducing a novel tool for process communication called delegate.

Main Results:

  • The BUILDER program successfully combines database searching and structure generation.
  • The delegate tool facilitates efficient process communication within the modeling environment.
  • Demonstrated the generation of novel molecular structures complementary to the HIV-1 protease active site.

Conclusions:

  • BUILDER offers a powerful new tool for receptor-based drug design.
  • The program facilitates the creation of diverse and complementary molecular structures.
  • This approach aids in the rational design of novel drug candidates for specific biological targets.