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

Blind Procedures02:07

Blind Procedures

12.5K
Ideally, the people who observe and record the children’s behavior are unaware of who was assigned to the experimental or control group, in order to control for experimenter bias. Experimenter bias refers to the possibility that a researcher’s expectations might skew the results of the study. Remember, conducting an experiment requires a lot of planning, and the people involved in the research project have a vested interest in supporting their hypotheses. If the observers knew which...
12.5K

You might also read

Related Articles

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

Sort by
Same author

RND/HAE-1 members in the Pseudomonadota phylum: exploring multidrug resistance.

Biophysical reviews·2025
Same author

Gene Expression and Prognostic Value of NADPH Oxidase Enzymes in Breast Cancer.

International journal of molecular sciences·2024
Same author

Key Topics in Molecular Docking for Drug Design.

International journal of molecular sciences·2019
Same author

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.

Journal of computer-aided molecular design·2018

Related Experiment Video

Updated: Nov 15, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

751

Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.

Paula Jofily1, Pedro G Pascutti1, Pedro H M Torres1

  • 1Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.

Molecules (Basel, Switzerland)
|March 6, 2021
PubMed
Summary
This summary is machine-generated.

We developed BLinDPyPr, a hybrid docking strategy that combines FTMap and DOCK6. This automated pipeline improves the speed and accuracy of small molecule binding site prediction for drug discovery.

Keywords:
blind dockingdock6ftmappipeline

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

611
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.2K

Related Experiment Videos

Last Updated: Nov 15, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

751
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

611
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

3.2K

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurately predicting small molecule binding sites on protein surfaces is crucial for drug discovery.
  • Current methods like blind docking and cavity detection-guided docking have limitations in terms of speed and accuracy.
  • A hybrid approach is needed to balance efficiency and precision in virtual screening.

Purpose of the Study:

  • To develop and validate BLinDPyPr, an automated pipeline for hybrid blind docking.
  • To improve the efficiency and accuracy of predicting small molecule binding sites and conformations.
  • To bridge the gap between conventional blind docking and cavity detection-guided docking methods.

Main Methods:

  • Developed BLinDPyPr, an automated pipeline integrating FTMap and DOCK6.
  • Utilized FTMap to generate probe clusters, converted them into DOCK6 spheres for binding region identification.
  • Implemented a hybrid blind docking strategy for simultaneous probing and selection of binding pockets based on ligand properties.

Main Results:

  • Achieved pose prediction success rates of 45.2-54.3%, comparable to site-specific docking.
  • The BLinDPyPr pipeline demonstrated a 50% reduction in time compared to conventional blind docking with DOCK6.
  • Successfully identified and prioritized potential binding regions based on ligand-specific properties.

Conclusions:

  • BLinDPyPr offers a practical and efficient solution for virtual screening of large molecule libraries.
  • The hybrid docking strategy enhances accuracy while significantly reducing computational time.
  • This method provides a valuable tool for accelerating drug discovery and development processes.