Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Inhibitors of Bacterial Protein Synthesis

Inhibitors of Bacterial Protein Synthesis

Aminoglycosides constitute a highly potent class of bactericidal antibiotics that exert their antimicrobial effects by targeting the bacterial ribosome, specifically disrupting protein synthesis. These polycationic molecules consist of amino-modified sugars linked via glycosidic bonds to an aminocyclitol core such as 2-deoxystreptamine or streptamine. Their strong positive charges facilitate tight binding to the negatively charged phosphate backbone of ribosomal RNA (rRNA), primarily at the 16S...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Structure and dynamics in drug discovery.

npj drug discovery·2026

Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026

Same author

Markovian state models uncover casein kinase 1 dynamics that govern circadian period.

Biophysical journal·2025

Same author

The need to implement FAIR principles in biomolecular simulations.

Nature methods·2025

Same author

Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period.

bioRxiv : the preprint server for biology·2025

Same author

The mechanism of allosteric regulation of calcium-independent phospholipase A<sub>2</sub> by ATP and calmodulin binding to the ankyrin domain.

Proceedings of the National Academy of Sciences of the United States of America·2024

Same journal

Probing Cinnamamides and Benzamides as Anthelmintics: Discovery of Potent Drug-Like Agents Against Angiostrongylus cantonensis.

Chemical biology & drug design·2026

Same journal

Perfluorooctane Sulfonate Exposure and Peripheral Artery Disease: Mendelian Randomization and Integrative Multi-Omics Systems Toxicology With Machine Learning.

Chemical biology & drug design·2026

Same journal

In Silico Drug Repositioning Identifies SYK Kinase Inhibitors as Potential Neuroprotective Agents for Ataxia-Telangiectasia.

Chemical biology & drug design·2026

Same journal

Synthesis of Peptide Analogs From Fish Venom With Potential Antimicrobial and Anticancer Activity.

Chemical biology & drug design·2026

Same journal

Design, Optimization and Mechanistic Insights Into Terpenoid-Derived Inhibitors of Protein Kinase C Iota.

Chemical biology & drug design·2026

Same journal

Design, Synthesis, and In Vitro Biological Assessment of Novel Benzimidazole and Hydrazone Derivatives Against Pancreatic Cancer and Melanoma Cells.

Chemical biology & drug design·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 25, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

AutoGrow: a novel algorithm for protein inhibitor design.

Jacob D Durrant¹, Rommie E Amaro, J Andrew McCammon

¹Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093-0365, USA. jdurrant@ucsd.edu

Chemical Biology & Drug Design

|February 12, 2009

Summary

This summary is machine-generated.

A new computer-aided drug design algorithm, AutoGrow, was developed by combining fragment-based growing and docking methods. This approach successfully recreated known drug ligands from smaller molecular fragments, demonstrating its potential in rational drug discovery.

More Related Videos

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

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

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

Published on: June 23, 2026

Related Experiment Videos

Last Updated: Jun 25, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

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

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

Published on: June 23, 2026

Area of Science:

Computational chemistry
Structural biology
Medicinal chemistry

Background:

Advances in protein crystallography and computing power have fueled computer-based rational drug design.
Existing algorithms optimize molecular interactions (hydrogen bond, electrostatic, hydrophobic) to identify potential drug candidates.
There is a need for novel algorithms that efficiently explore chemical space for drug discovery.

Purpose of the Study:

To introduce AutoGrow, a novel computer-aided drug design algorithm.
To combine fragment-based growing and molecular docking strategies for enhanced ligand design.
To validate the AutoGrow algorithm's efficacy in drug design.

Main Methods:

Development of the AutoGrow algorithm, integrating fragment-based growing and docking.
In silico generation of potential drug ligands by optimizing molecular interactions.
Validation using crystallographically resolved protein-ligand complexes.

Main Results:

AutoGrow successfully recreated three known crystallographically resolved ligands from their constituent fragments.
The algorithm demonstrates the ability to assemble complex ligands from smaller building blocks.
Successful reconstruction validates the computational approach for drug design.

Conclusions:

AutoGrow represents a novel and effective approach for computer-aided drug design.
The algorithm's ability to reconstruct known ligands highlights its potential for identifying new drug candidates.
This method offers a promising avenue for accelerating the drug discovery process.