Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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...
Protein-protein Interfaces02:04

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...
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...

You might also read

Related Articles

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

Sort by
Same author

Probing 3-Amino-2H-Azaindazoles as Allosteric Inhibitors of the Protein Tyrosine Phosphatase SHP2.

ChemMedChem·2026
Same author

Fragment-Based Design of Targeted Covalent Inhibitors: The Scope and Limitation of Linking Approaches.

ChemMedChem·2026
Same author

α-Halothioamide warheads with enhanced cysteine reactivity and specificity for covalent protein labelling.

Nature communications·2026
Same author

Merging Micellar Catalysis and C-H Activation: Silver-Free Direct Arylation of Fluoroarenes in Water.

ChemSusChem·2026
Same author

Mapping the SHP2 Allosteric Pocket With Target-Biased Covalent Fragments.

Chembiochem : a European journal of chemical biology·2026
Same author

Efficiency landscape of bioorthogonal click reactions producing bispecific antibody conjugates.

Cell reports methods·2026

Related Experiment Video

Updated: Jun 13, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes.

Márk Sándor1, Róbert Kiss, György M Keseru

  • 1Discovery Chemistry, Gedeon Richter plc., P.O. Box 27, H-1475 Budapest, Hungary.

Journal of Chemical Information and Modeling
|May 13, 2010
PubMed
Summary

Glide docking accuracy was assessed for protein-fragment complexes. Standard precision (Glide SP) protocols excelled, achieving accurate poses and effective sampling for fragment docking, though scoring schemes require further development.

More Related Videos

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Related Experiment Videos

Last Updated: Jun 13, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurate protein-ligand pose prediction is crucial for drug discovery.
  • Glide is a widely used molecular docking software.
  • Evaluating docking protocols is essential for optimizing virtual screening strategies.

Purpose of the Study:

  • To assess the docking accuracy of the Glide software using various protocols.
  • To compare the performance of different Glide docking protocols for protein-fragment complexes.
  • To identify limitations and areas for improvement in Glide's fragment docking capabilities.

Main Methods:

  • Evaluated 16 docking protocols on 190 protein-fragment complexes across 78 targets.
  • Utilized standard precision (Glide SP) and extra precision (Glide XP) docking.
  • Performed cross-docking experiments and analyzed root-mean-square deviation (rmsd) and success rates.

Main Results:

  • Glide SP protocols demonstrated the best performance with an average rmsd of 1.17 Å for 80% of complexes within 2 Å.
  • Glide's sampling efficacy is adequate for fragment docking, but scoring schemes may limit accuracy.
  • Cross-docking with Glide SP yielded comparable results to Glide XP, with significant improvements when selecting optimal X-ray structures.

Conclusions:

  • Standard precision Glide SP is effective for fragment docking, achieving high accuracy in pose prediction.
  • Scoring functions represent a bottleneck for Glide's docking accuracy, as indicated by weak correlation with binding affinities.
  • Optimizing X-ray structure selection is critical for enhancing the success of virtual fragment screening using molecular docking.